Tag: fastq

What should I do with the fastq files of negative controls? – General Discussion

I am using QIIME2 and R packages for microbiome analysis.I think QIIME2 is the best tool, especially for researchers who are about to begin the microbiome analysis. My question is about the decontamination process. I have the fastq files of 16s microbiome sequences from skin tissue samples. The sequence files…

Continue Reading What should I do with the fastq files of negative controls? – General Discussion

Cost-effective and accurate genomics analysis with Sentieon on AWS

This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…

Continue Reading Cost-effective and accurate genomics analysis with Sentieon on AWS

MGI Makes its Mark in Dubai with Latest Platforms at MEDLAB Middle East and Arab Health

DUBAI, UAE, Jan. 30, 2023 /PRNewswire/ —  MGI Tech Co., Ltd. (“MGI”), a company committed to building core tools and technology to lead life science, will introduce many of its latest gene sequencing platforms and sample preparation system at MEDLAB Middle East 2023, taking place 6-9 February in Dubai. Ahead of…

Continue Reading MGI Makes its Mark in Dubai with Latest Platforms at MEDLAB Middle East and Arab Health

Merging FASTQs from the same sample

Merging FASTQs from the same sample 0 Hello, I have a question regarding merging FASTQ files from the same sample but different sequencing runs. We generated cDNA libraries using the 10X v3 protocol but weren’t sure they had worked so initially sequenced only a small fraction of the library (10,000…

Continue Reading Merging FASTQs from the same sample

Problem using SRAtoolkit

Problem using SRAtoolkit 1 Hello Biostars community I wanted to use split-3 function of sratoolkit to split my pair-ended RNA-seq files to two fastq files. However, after inserting the code, I get the following error. What is the problem? ./fastq-dump –split-3 2023-01-29T12:54:14 fastq-dump.3.0.2 err: param empty while validating argument list…

Continue Reading Problem using SRAtoolkit

transcriptomincs

transcriptomincs 1 Hi, can I assemble transcripts sequence (fastq) of one species by taking other species genome (belongs to same genus) as reference genome? thanks in advance assembly transcriptome • 145 views • link updated 1 hour ago by GenoMax 125k • written 1 day ago by Kiran • 0…

Continue Reading transcriptomincs

maximum fastq file size in galaxy?

maximum fastq file size in galaxy? 0 Hello I got a couple of miRNA-seq fastqs and I uploaded them on galaxy as a paired collection. One of my fastqs, however, is much larger than the others, as they range from 600mb to 2.4gb, but one sample has 27gb. When I…

Continue Reading maximum fastq file size in galaxy?

Error 134 while aligning using hisat2

Error 134 while aligning using hisat2 0 Hello, I am using the below command to align the reads and get bam file: hisat2 -x /hisat/grch38/genome -1 /fastq/output_forward_paired.fq.gz -2 /fastq/output_reverse_paired.fq.gz | samtools sort -o /bams/outout.bam This was running perfectly ok for the last try, however, for the new try I got…

Continue Reading Error 134 while aligning using hisat2

counting reads in a fastq file using a refrence fasta file

counting reads in a fastq file using a refrence fasta file 1 Hi I have a reference fasta file containing 130,000 unique sequences (barcodes), each 30nts long. These sequences were synthesized with random incorporation of nucleotides in each position, so they have very large hamming distance. I had a pool…

Continue Reading counting reads in a fastq file using a refrence fasta file

Species richness of bat flies and their associations with host bats in a subtropical East Asian region | Parasites & Vectors

Scott M, Dobson A. The role of parasites in regulating host abundance. Parasitol Today. 1989;5:176–83. CAS  Google Scholar  Tompkins D, Dobson A, Arneberg P, Begon M, Cattadori I, Greenman J, et al. Parasites and host population dynamics. The ecology of wildlife diseases. 2002; 45–62. Thomas F, Poulin R, Brodeur J….

Continue Reading Species richness of bat flies and their associations with host bats in a subtropical East Asian region | Parasites & Vectors

transcriptome assembly, GWA, BGC

transcriptome assembly, GWA, BGC 0 HI, I have denovo transcriptome assembled file of a plant, I want to see the gene cluster for terpens. I do have genome data of related species which belongs to same genera. My 1st query is, can I use denovo assembled data for locate gene…

Continue Reading transcriptome assembly, GWA, BGC

HISAT2 output direct to bam sorted

HISAT2 output direct to bam sorted 0 Hi all, I am mapping my samples to a reference genome with HISAT2 and I was wondering if it is possible to get the outputs in bam format and also if it is possible to sort by coordinates directly? Could you help me…

Continue Reading HISAT2 output direct to bam sorted

bwa-meth unrecognized reference name during sam_parse

bwa-meth unrecognized reference name during sam_parse 0 Dear all, I have some Enzymatic methyl sequencing data that I am trying to align using bwa-meth (github.com/brentp/bwa-meth). However, I am encountering the following issue in parsing of the sam file that the aligner is generating when I try to convert the sam…

Continue Reading bwa-meth unrecognized reference name during sam_parse

How to compare a Nanopore read (.fastq) to a genome assembly file (.fna)

How to compare a Nanopore read (.fastq) to a genome assembly file (.fna) 0 Hi, I want to compare a Nanopore read in fastq format to a reference genome file of an animal in fna format in order to determine whatever the read came from this animal DNA. What are…

Continue Reading How to compare a Nanopore read (.fastq) to a genome assembly file (.fna)

error making Txdb from GTF and fasta files

Hello, I would like to use ORFik to map Ribo-reads to different ORFs in the maize genome. The latest version of the genome is Zm-B73-REFERENCE-NAM-5.0.fa. The annotation file is a GFF3. I have the genome fasta file, the fasta fai file, and the GFF3 file. The ORFik package uses GTF…

Continue Reading error making Txdb from GTF and fasta files

Calculate sequencing file size?

Calculate sequencing file size? 0 We are writing the data management plan and I need to estimate the size of the data we’ll get (for storage costs) per sample (as a fastq.gz). I found a very rough estimation in this comment which is what I know from previous experience, but…

Continue Reading Calculate sequencing file size?

Normalizing TCR data

Normalizing TCR data 1 Hi, What’s the best method to normalize TCR repertoire data (for comparison between samples) which already has raw counts and count frequency. Already tried Counts per Million (CPM) but there’s a possibility that it might exaggerate the count number of a clone so the real picture…

Continue Reading Normalizing TCR data

PHG Load haplotype and create consensus

Here, presented my PHG scripts, config, wgs_keyfile. 1. Create valid intervals docker run –name test_assemblies –rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t maizegenetics/phg:1.0 /tassel-5-standalone/run_pipeline.pl -Xmx100G -debug -configParameters /phg/Masterconfig.txt -CreateValidIntervalsFilePlugin -intervalsFile /phg/inputDir/reference/glyma.Wm82.gnm4.ann1.T8TQ.gene_models_main.bed -referenceFasta /phg/inputDir/reference/glyma.Wm82.gnm4.4PTR.genome_main.fixed.fna.gz -mergeOverlaps true -generatedFile /phg/validBedFile.bed -endPlugin &> Log/1.Create_validinterval.txt & 2. Create initial DB docker run –name create_initial_db –rm -v /DATA/jysong/PHG/ver1.0_phg/:/phg/ -t…

Continue Reading PHG Load haplotype and create consensus

Difference between python and biopython

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

Continue Reading Difference between python and biopython

Redirect output from MIXCR

Redirect output from MIXCR 2 If your command is: mixcr analyze amplicon -s <species> \ –starting-material <startingmaterial> \ –5-end <5End> –3-end <3End> \ –adapters <adapters> \ [OPTIONS] input_file1 [input_file2] analysis_name then set analysis_name as path/to/analysis/analysis_name Just add the path as a part of the prefix for output files: e.g. mixcr…

Continue Reading Redirect output from MIXCR

Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq)

Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq) 1 Hello, I used MIXCR on standard Single Cell data and found some common clonotypes among my multiple conditions. I would like to know if it would be possible to track clonotypes with the TCR Sequence ? If…

Continue Reading Track Clonotypes with TCR Sequence on standard Single Cell data (not scTCR-Seq)

Comparing 5’RACE TCR Sequencing Methods

Comparing 5’RACE TCR Sequencing Methods 1 Hello, My laboratory developed an in-house 5’RACE method with custom primers targeting the constant region of the gamma/delta T cells. We submitted RNA to a third party commercial laboratory to benchmark our method against their 5’RACE method. Both our in-house fastq’s and the third…

Continue Reading Comparing 5’RACE TCR Sequencing Methods

Low alignment rates for randomly shredded TCR-B library with MixCR

Low alignment rates for randomly shredded TCR-B library with MixCR 1 Hello community, Apologies for cross-posting my query here along with the github page for MixCR. I am hoping to seek help from a wider community here. I recently applied the MiXCR pipeline in ‘shotgun’ mode to analyze my randomly…

Continue Reading Low alignment rates for randomly shredded TCR-B library with MixCR

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Pfeffer C, Larsen S, Song J, Dong M, Besenbacher F, Meyer RL, et al. Filamentous bacteria transport electrons over centimetre distances. Nature. 2012;491:218–21. Article  CAS  Google Scholar  Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol. 2022;20:5–19. Article  CAS  Google Scholar  Bjerg JT, Boschker…

Continue Reading Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Combine files that have partial filename matches

Combine files that have partial filename matches 1 Hi there, I have multiple sequencing reads with the following structure (the below is just an example): > MSP3_run719_TCATCCTA_S65_L004_R1_001.fastq.gz > MSP3_run720_TCATCCTA_S45_L001_R1_001.fastq.gz > MSP3_run720_TCATCCTA_S45_L002_R1_001.fastq.gz > MSP3_run719_TCATCCTA_S65_L004_R2_001.fastq.gz > MSP3_run720_TCATCCTA_S45_L001_R2_001.fastq.gz > MSP3_run720_TCATCCTA_S45_L002_R2_001.fastq.gz My goal is to combine reads that have the same names in columns…

Continue Reading Combine files that have partial filename matches

BULK mRNA-seq with UMIs. Do I need to normalize by gene length?

Hi, I am analyzed some BULK mRNA-seq data that included UMIs during the sequencing. I don’t have much experience analyzing bulk RNA-seq, and it is my first time dealing with UMIs there. I have more experience in single-cell RNA-seq, and I thought that the concept of UMIs will translate directly…

Continue Reading BULK mRNA-seq with UMIs. Do I need to normalize by gene length?

Error in trimmomatic

Error in trimmomatic 1 Hi! Trust you are well. I am trying to run this program but I get the following error and I dont know to fix it neither understand it. Could you help me please? java -jar trimmomatic-0.36.jar PE -phred33 white_replicate1.R1paired.fq.gz white_replicate1.R2paired.fq.gz white_replicate1.R1paired.fq.gz white_replicate1.R1unpaired.fq.gz white_replicate1.R2paired.fq.gz white_replicate1.R2unpaired.fq.gz ILLUMINACLIP:/mnt/g/poolseq_tutorial_1/poolseq_tutorial/adapters/TruSeq3- PE.fa:2:20:10:1:true…

Continue Reading Error in trimmomatic

Analysis of Smart-Seq3 data with kallisto-bustools

Tutorial:Analysis of Smart-Seq3 data with kallisto-bustools 0 Based on @dsull’s answer. The smart-seq3 analysis is handled by the kallisto-bustools pipeline. Create a conda environment if needed. Create the conda environment file and save it as env_kb.yml. # conda environment for kallisto bustools pipeline name: kb channels: – bioconda – conda-forge…

Continue Reading Analysis of Smart-Seq3 data with kallisto-bustools

cutadapt installed via conda igzip error for some fastq files

Only very recently (~2 weeks ago), cutadapt installed via conda has the following error: This is cutadapt 3.2 with Python 3.8.6 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC in2438_3_CKDL210000739-2a-AK5142-AK6697_HVHF2DSXY_L2_1.fq.gz Processing reads on 4 cores in single-end mode … [———>8 ] 00:00:26 5,536,084 reads @…

Continue Reading cutadapt installed via conda igzip error for some fastq files

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….

Continue Reading Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

zero byte files in sratoolkit.3.0.1-ubuntu64

zero byte files in sratoolkit.3.0.1-ubuntu64 0 I have downloaded sratoolkit for ubuntu. After getting the tar file and unzip it, I added the bin path to the Path variables as well. When I run which fastq-dump, it correctly identifies the path. However, when I run vdb-config -i or vdb-config –interactive…

Continue Reading zero byte files in sratoolkit.3.0.1-ubuntu64

Extracting list of target genes from ChIP-seq bigwig file

Extracting list of target genes from ChIP-seq bigwig file 1 I am reading a publication where the authors performed ChIP-seq on a specific TF. Their data was deposited on NCBI in bigwig format. I would like to extract the final list of target genes. Is this possible using the bigwig…

Continue Reading Extracting list of target genes from ChIP-seq bigwig file

htslib/c what is the correct way to use bgzf_thread_pool ?

htslib/c what is the correct way to use bgzf_thread_pool ? 1 I try to split fastq files into ‘N’ chunks using a simple CC program and htslib-C . It works fine: ./split2file -o TMP S1.R1.fq.gz S1.R2.fq.gz -n 10 but when I use a thread pool ( As far as I…

Continue Reading htslib/c what is the correct way to use bgzf_thread_pool ?

Trimmomatic can’t find the adapter files

Trimmomatic can’t find the adapter files 0 Trimmomatic can’t seem to find my adapter files, and I’ve tried a lot of different pathways but nothing works. Any help is appreciated, thanks. Here’s my code: for file in ../../fqgz_trim_single/*R1_001.fastq.gz; do trimmomatic SE -threads 1 -phred33 -trimlog $file ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15…

Continue Reading Trimmomatic can’t find the adapter files

Bulk RNA seq with deseq2, rnaseqGene, or edgeR

Bulk RNA seq with deseq2, rnaseqGene, or edgeR 0 @fdd03415 Last seen 1 day ago United States Hi, This might be a very simple question but I am new to bulkRNAseq and would like to analyze paired FastQ files with DESeq2, rnaseqGene, or edgeR. Could anyone provide me with some…

Continue Reading Bulk RNA seq with deseq2, rnaseqGene, or edgeR

Standards, Regulation, Funding Move Bioinformatics in 2022, But Hurdles to Precision Medicine Remain

CHICAGO – Although the US Food and Drug Administration (FDA) provided some long-sought clarity in 2022 on how it would regulate clinical decision support and in vitro diagnostic software, technology developers and healthcare organizations still struggled with how to integrate genomics data into clinical practice. It will likely take more…

Continue Reading Standards, Regulation, Funding Move Bioinformatics in 2022, But Hurdles to Precision Medicine Remain

Test DSSP generation from MMCIF with non-standard residues.

Hi Maarten, This seems to stem from your latest upload of dssp. Could you consider taking a look at this one? Thanks, Nilesh On Sun, 1 Jan 2023 15:20:12 +0100 Lucas Nussbaum <lu…@debian.org> wrote: > Source: python-biopython > Version: 1.80+dfsg-4 > Severity: serious > Justification: FTBFS > Tags: bookworm sid ftbfs > User: lu…@debian.org > Usertags: ftbfs-20230101 ftbfs-bookworm > >…

Continue Reading Test DSSP generation from MMCIF with non-standard residues.

A multi-omics integrative network map of maize

Eisenstein, M. Big data: the power of petabytes. Nature 527, S2–S4 (2015). Article  CAS  Google Scholar  Trewavas, A. A brief history of systems biology: ‘Every object that biology studies is a system of systems’. Francois Jacob (1974). Plant Cell 18, 2420–2430 (2006). Article  CAS  Google Scholar  Dixon, S. J., Costanzo,…

Continue Reading A multi-omics integrative network map of maize

ChIP-seq problem

ChIP-seq problem 0 Hello, I have just uploaded two bw files to IGV, they are from the same experiment, only the second one was sequenced more. When I load them more I notice that the file sequenced more has peaks that are lower, why is that in your opinion? N.B….

Continue Reading ChIP-seq problem

Analyzing time-series RNA-seq data using DEseq2

Analyzing time-series RNA-seq data using DEseq2 1 Hello everyone, I need a direction in using DEseq2. my Input : I have RNAseq data from two groups of mice (groups based on type of bacterial treatment). Each group was harvested at 7 different time points. In other words I have two…

Continue Reading Analyzing time-series RNA-seq data using DEseq2

Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment

Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…

Continue Reading Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment

minimap2, before or after assembly?

minimap2, before or after assembly? 1 Dear all, I feel confused because I saw someone uses the minimap2 after demultiplexing, but before proceeding with the assembly (CANU) [case 1], and someone using the minimap2/samfile/BFCTools/medaka after assembly (always CANU) [case 2]. In case 1, the reference file used to align against…

Continue Reading minimap2, before or after assembly?

Compressing BAM, SAM, CRAM | Genozip

How good is Genozip at compressing BAM files? ​ See Benchmarks. ​ Compressing a BAM, SAM or CRAM file  ​ In the rest of this page we will give examples of BAM files. Genozip is also capable of compressing SAM files, and with some limitations, CRAM files as well. ​…

Continue Reading Compressing BAM, SAM, CRAM | Genozip

Genome Bioinformatics Analyst at UPMC

Description The Genome Bioinformatics Analyst works independently to curate disease, gene and variant knowledge including variant interpretation, reporting and consultation with laboratory staff, physicians and genetic counselors. The analyst participates in clinical test development, validation and maintenance of data analysis pipelines, monitoring of quality metrics and the analysis of large…

Continue Reading Genome Bioinformatics Analyst at UPMC

Bioinformatics Analyst II (Remote) Position In North Chicago, IL

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: We have an exciting contract opportunity for a Bioinformatics analyst…

Continue Reading Bioinformatics Analyst II (Remote) Position In North Chicago, IL

Extra-hematopoietic immunomodulatory role of the guanine-exchange factor DOCK2

Cell isolation, reprogramming and culture Approval was obtained for human cell and tissue sample collection and genetic reprogramming from the Institutional Review Board (protocols 19–252, 18–243, 21–060, 19–284 and 415-E/1776/4-2014, Ethics Committee of the province of Salzburg). Adult samples were collected in accordance with the Declaration of Helsinki after written…

Continue Reading Extra-hematopoietic immunomodulatory role of the guanine-exchange factor DOCK2

parallel-fastq-dump install failed

parallel-fastq-dump install failed 0 Good morning, I am trying to install parallel-fastq-dump but I failed. And here is what ssh sever say: conda install parallel-fastq-dump Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current…

Continue Reading parallel-fastq-dump install failed

Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand

Kumarasamy, K. K. et al. Emergence of a new antibiotic resistance mechanism in India Pakistan, and the UK: A molecular, biological, and epidemiological study. Lancet Infect. Dis. 10, 597–602 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  Munoz-Price, L. S. et al. Clinical epidemiology of the global expansion of Klebsiella…

Continue Reading Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand

java – I am unable to execute the fastqc command in HPC cluster

I am trying to run fastqc for fastq.gz files in RNA-seq Data analysis and I have written a PBS script. However, I am encountering the following error Can’t exec “java”: No such file or directory at /home/paksls/Atreya/software/FastQC/fastqc line 307 I have written the following script: #!/bin/bash #PBS -l nodes=1:ppn=6,pmem=10240MB,walltime=04:00:00 #PBS…

Continue Reading java – I am unable to execute the fastqc command in HPC cluster

Samtools Convert Sam To Bam With Code Examples

Samtools Convert Sam To Bam With Code Examples In this session, we’ll try our hand at solving the Samtools Convert Sam To Bam puzzle by using the computer language. The code that follows serves to illustrate this point. # Basic syntax: samtools view -S -b sam_file.sam > bam_file.bam # Where:…

Continue Reading Samtools Convert Sam To Bam With Code Examples

Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

Continue Reading Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Converting Bam file to Fasta (Zipped)

Converting Bam file to Fasta (Zipped) 0 I would like to convert .bam files to fq.gz (zipped fasta files) for paired reads. bedtools bamtofastq seems to be a commonly recommended method, I have also seen samtools fastq as a possible alternative. bedtools bamtofastq -i inputfile.bam -fq outputR1.fq -fq2 outputR2.fq samtools…

Continue Reading Converting Bam file to Fasta (Zipped)

separate read1 and read2 from merged fastq file and align against reference genome

separate read1 and read2 from merged fastq file and align against reference genome 0 Hi, I am processing a merged fastq file. I used the following command to separate read1s and read2s in separate files for alignment using bwa mem. paste – – – – – – – – <…

Continue Reading separate read1 and read2 from merged fastq file and align against reference genome

BCL compression

BCL compression 2 Hi, I’m trying to store some RUNs generated by different Illumina sequencers. My idea is to compress them to keep all files together (and reduce size, but this is secondary)… however, because the big amount of files and because the global size can be enormous (~120GB!) I’m…

Continue Reading BCL compression

sra-toolkit not working

sra-toolkit not working 2 I downloaded sra-toolkit from sra website for 64bit Windows. After extracting I tested it from bin folder: sra-toolkit\bin> fastq-dump –stdout -X 2 SRR390728 but it throws error: 2015-12-15T09:54:40 fastq-dump.2.5.5 err: item not found while constructing within virtual database module – the path ‘SRR390728’ cannot be opened…

Continue Reading sra-toolkit not working

Combine scRNAseq data for bulk analysis using DESeq2

Combine scRNAseq data for bulk analysis using DESeq2 0 @evocanres-17914 Last seen 2 hours ago United States I have scRNAseq data from Fluidigm C1 platform, but I have low number of cells (sample 1 ~30, sample 2 ~ 20). Can I merge the fastq files for each samples and treat…

Continue Reading Combine scRNAseq data for bulk analysis using DESeq2

Microbiome Functionality with QIIME2 – General Discussion

otrujillor (Otrujillor) October 5, 2022, 5:11am #1 Is there any way to analyze the microbiome functionality with QIIME2.I have the following files: metadata.tsv the forward reads (****_L001_R1_001.fastq.gz) the reverse reads (****_L001_R2_001.fastq.gz) And I have already imported my data into QIIME2 and got the *.qza file.I performed the sequence quality control…

Continue Reading Microbiome Functionality with QIIME2 – General Discussion

Bedtools Bam To Bed With Code Examples

Bedtools Bam To Bed With Code Examples With this article, we’ll look at some examples of how to address the Bedtools Bam To Bed problem . bedtools bamtobed [OPTIONS] -i <BAM> As we have seen, a large number of examples were utilised in order to solve the Bedtools Bam To…

Continue Reading Bedtools Bam To Bed With Code Examples

Order of reads in Long read FASTQ file

Order of reads in Long read FASTQ file 0 Hi all, FASTQ files contain sequencing reads ‘as they come off the sequencing instrument.’ Is there any particular order to them in long read fastq file for ONT and PacBio? E.g. based on the position of the flow cell? Quality? I…

Continue Reading Order of reads in Long read FASTQ file

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…

Continue Reading How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

HISAT2 and HTSEQ command

HISAT2 and HTSEQ command 0 @4fedfa78 Last seen 10 hours ago Japan Hello, For analysis of the data by rna-sequencing I selected HISAT2 and HTSeq-count for mapping and counting the genes levels, the libraryLayout is paired, I am using the below command for both but the results are not exact…

Continue Reading HISAT2 and HTSEQ command

Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

Continue Reading Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

Comment: How to resolve a ValueError: Multiple 'HD' Lines are not permitted when I run Ci

I tried your suggestion **samtools view -H qname_unknown_circle.bam** and the output result is like this: yu@root:~$ samtools view -H qname_unknown_circle.bam @HD VN:1.5 SO:queryname @SQ SN:chr1 LN:248956422 @SQ SN:chr10 LN:133797422 @SQ SN:chr11 LN:135086622 ………(Many lines like this ‘@SQ SN:chrxx LN:xxxx’ are omitted) @SQ SN:chrY_KI270740v1_random LN:37240 @HD VN:1.5 SO:unsorted GO:query @PG ID:bwa…

Continue Reading Comment: How to resolve a ValueError: Multiple 'HD' Lines are not permitted when I run Ci

Run fastqc reports for each of the fastq files in:

Run fastqc reports for each of the fastq files in: /data/CompRes/seq_platform_data/ To run the fastqc reports, you can write a script that will execute the following command (edited for you) for each file: fastqc /data/CompRes/seq_platform_data/<inputfastq> -o /home/ASURITE/BIO439/module4/ Then transfer the html files to your local computer and view them, so…

Continue Reading Run fastqc reports for each of the fastq files in:

CNV Pipeline Options

The following are the top-level options that are shared with the DRAGEN Host Software to control the CNV pipeline. You can input a BAM or CRAM file into the CNV pipeline. If you are using the DRAGEN mapper and aligner, you can use FASTQ files. …

Continue Reading CNV Pipeline Options

Bioinformatics Scientist in Pittsburgh, PA

Description Purpose:The scientist works independently using a robust math toolbox to discover solutions for a diverse portfolio of interesting and challenging problems. The scientist develops, implements, and monitors advanced analytic, medical informatics, and predictive modeling tools for health care programs at the UPMC. The scientist normally works Monday through Friday…

Continue Reading Bioinformatics Scientist in Pittsburgh, PA

DRAGEN .bcl conversion error due to improper custom p5 oligos

DRAGEN .bcl conversion error due to improper custom p5 oligos 0 I am working on a custom library preparation method and I designed my p5 oligos incorrectly. To be specific, I used the reverse complement of the correct p5 index sequence. As a result my fastq files aren’t demultiplexing properly….

Continue Reading DRAGEN .bcl conversion error due to improper custom p5 oligos

Understanding bam tracks

Understanding bam tracks 0 Sorry i am having trouble understanding this concept. For example, when I view a bam file after alignment in igv, I see that there are different tracks that form. How are these tracks formed/why do some aligned sequences belong together or are part of the same…

Continue Reading Understanding bam tracks

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

Continue Reading Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

What is the Difference Between FASTA and FASTQ

The key difference between FASTA and FASTQ is that FASTA is a text-based format that only stores nucleotide or protein sequences, while FASTQ is a text-based format that stores both sequence and associated sequence quality values. Bioinformatics is a field that uses different software to analyse and understand biological data,…

Continue Reading What is the Difference Between FASTA and FASTQ

iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

Continue Reading iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

Continue Reading mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

Patrick Murphy Bulk RNA-Seq – HackMD

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

Continue Reading Patrick Murphy Bulk RNA-Seq – HackMD

TPM normalization starting with read counts

Hello everyone I have multiple bulk RNA-seq datasets that I need to apply the same pipe line on. I want to normalize them from counts data to TPM. In all datasets, I have the genes as rows, and samples as columns. Unfortunately, I don’t have the fastq files, all I…

Continue Reading TPM normalization starting with read counts

Setting up Aspera Connect (ascp) on Linux and macOS

This tiny tutorial cover setting up Aspera Connect (binary is called ascp) which might be used to download sequencing data, e.g. with download links provided by sra-explorer.info, see also sra-explorer : find SRA and FastQ download URLs in a couple of clicks Setting up Aspera Connect is simple and was…

Continue Reading Setting up Aspera Connect (ascp) on Linux and macOS

ViReMa not working after adapter trimming

ViReMa not working after adapter trimming 0 Hi, I have a viral RNA-seq dataset that I am trying to run through ViReMa to look for deletion junctions. When I input my fastq files directly into ViReMa without trimming adapters first, my results look about how I would expect (multiple junctions…

Continue Reading ViReMa not working after adapter trimming

Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

Continue Reading Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth

Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…

Continue Reading Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

I have a query regarding differential gene expression using limma-voom.

I have a query regarding differential gene expression using limma-voom. 1 @28946033 Last seen 1 day ago India I used the following pipeline for RNA Seq Analysis Fastq-Trimmomatic- Hisat2(gtf file was annotated)-featurecounts After featurecounts I tried to do limmavoom, but I get error saying this An error occurred with this…

Continue Reading I have a query regarding differential gene expression using limma-voom.

Could not locate a HISAT2 index to basename

Could not locate a HISAT2 index to basename 2 First time trying out HISAT2 and I’m having a problem here, even with the pre-made indices for GRCH38. $ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam Error follows Could not locate a HISAT2 index corresponding to basename “/share/projects/RNASeq/data/reference/GRCh38/grch38_tran” Error:…

Continue Reading Could not locate a HISAT2 index to basename

Samtools Htslib Issues

Issue Title State Comments Created Date Updated Date How to get a specific chromosome open 1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times open 4 2022-07-11 2022-07-18 Modified base parsing failure failure closed 0 2022-07-01 2022-07-18 extract genotype information open 1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if…

Continue Reading Samtools Htslib Issues

Error in Importing data in qiime2

Error in Importing data in qiime2 0 Hello All, I am trying to provide an input of my amplicon sequencing files which are in .fq format for qiime2 and I am getting error There was a problem importing fastqcpwo: Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: ‘.+_.+_L[0-9][0-9][0-9]_R[12]_001\\.fastq\\.gz’ Can someone please…

Continue Reading Error in Importing data in qiime2

BWA alignment/Samtools; Fail to read the header

BWA alignment/Samtools; Fail to read the header 0 Hello, I have an issue with my alignment. This is an error in my log file: fail to read the header from “-“. Here is my script: bwa mem -t 8 -R “@RG\tID:$2\tSM:$3” ~/scratch/pt6/pt6.fa ${1}_1.fastq.gz ${1}_2.fastq.gz 2>log.bwa_new.$1 |samtools view -S -h -b…

Continue Reading BWA alignment/Samtools; Fail to read the header

PeerJ expertRxiv – Postdoctoral Associate in Bioinformatics

Job description Location: Boca Raton, Florida Job Description: The College of Medicine of Florida Atlantic University, the 5th public university in Florida, is seeking a Bioinformatics Postdoctoral Associate with experience in bioinformatics pipeline development and genomics data analysis for a Bioinformatics and Computational Genomics laboratory which focuses on high-throughput…

Continue Reading PeerJ expertRxiv – Postdoctoral Associate in Bioinformatics

Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

Software official website : Hisat2: Manual | HISAT2 StringTie:StringTie article :Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial : 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

Continue Reading Hisat2 – stringtie – deseq2 pipeline for bulk RNA seq

Differing number of reads for read 1 and 2 in fastq’s from a subset bam file

I’m working with paired-end wgs data I downloaded from TCGA. I’m trying to extract the reads that align to a specific region, extract only those reads to two fastq files, one for each pair. Unfortunately, I am getting a different number of reads in both fastq files because some of…

Continue Reading Differing number of reads for read 1 and 2 in fastq’s from a subset bam file

Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment | BMC Infectious Diseases

Mokomane M, Kasvosve I, Melo Ed, Pernica JM, Goldfarb DM. The global problem of childhood diarrhoeal diseases: emerging strategies in prevention and management. Ther Adv Infect Dis. 2018;5(1):29–43. PubMed  Google Scholar  Organization WH. Rotavirus vaccines: WHO position paper–July 2021. Weekly Epidemiol Rec. 2021;96(28):301–219. Google Scholar  Bucardo F, Reyes Y, Svensson…

Continue Reading Genetic characterization of two G8P[8] rotavirus strains isolated in Guangzhou, China, in 2020/21: evidence of genome reassortment | BMC Infectious Diseases

Pooled shRNA Library Screening to Identify Factors that Modulate a Drug Resistance Phenotype

High-throughput RNA interference (RNAi) screening using a pool of lentiviral shRNAs can be a tool to detect therapeutically relevant synthetic lethal targets in malignancies. We provide a pooled shRNA screening approach to investigate the epigenetic effectors in acute myeloid leukemia (AML). The overall goal of the following video is to…

Continue Reading Pooled shRNA Library Screening to Identify Factors that Modulate a Drug Resistance Phenotype

How To Download Geo Data? Update New

Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Images related to the topicBioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics…

Continue Reading How To Download Geo Data? Update New

bgzf_read_block] EOF marker is absent reformat.sh

BBMap/BBTools reformat.sh : real error or spurious message? [W::bgzf_read_block] EOF marker is absent reformat.sh 1 When subsampling paired-end .fastq.gz files using reformat.sh from BBMap/BBTools, I get this error message: [W::bgzf_read_block] EOF marker is absent reformat.sh I’ve checked the input files with gunzip -t, no error. The input files are a…

Continue Reading bgzf_read_block] EOF marker is absent reformat.sh

Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

Continue Reading Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Detailed differences between sambamba and samtools

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ?, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

Continue Reading Detailed differences between sambamba and samtools

Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar  Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article  Google Scholar  Odland,…

Continue Reading Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

[W::bgzf_read_block] EOF marker is absent in BBMAP

[W::bgzf_read_block] EOF marker is absent in BBMAP 0 Hello, I’m asking an issue encountered in bbmap. I was using bbmap to remove host contaminants from my microbiome data. The commands are simple as below (ref folder already generated in the last step) bbmap.sh -Xmx42g in=R1.fastq.gz in2=R2.fastq.gz outu=cleaned.interleaved.fastq.gz threads=12 overwrite=t unpigz=t…

Continue Reading [W::bgzf_read_block] EOF marker is absent in BBMAP

Strange Per base sequence content of fastqc

Hi, all! I download fastq.gz files of GSE162708 from ENA which only have 2 files of each sample(usually scRNA-seq has 3 files I1 , R1 & R2 ). Then I run fastp as following Then I get QC report , but I can’t understand why Per base sequence content of…

Continue Reading Strange Per base sequence content of fastqc

tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…

Continue Reading tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics

FastQ_7 April 2022(1) – Copy.pptx – What is the FASTA format? The FASTA format is the “workhorse” of bioinformatics. It is used to represent sequence

the FASTA format is not “officially” defined – even though it carries the majority of data information onliving systems. Its origins go back to asoftware tool calledFastawritten byDavidLipman(ascientist that later became, and still is, the director of NCBI) andWilliam R. Pearsonof the University ofVirginia. The tool itself has (to some…

Continue Reading FastQ_7 April 2022(1) – Copy.pptx – What is the FASTA format? The FASTA format is the “workhorse” of bioinformatics. It is used to represent sequence

Reference-based alignment using MUSKET

Reference-based alignment using MUSKET 1 I’m running MUSKET on my dataset trimmed_data.tar.gz using 1000 threads, 2000 threads, and 4000 threads on a HPC. I’ve been unable to obtain any results because the software seems to be running for a long time. ./../musket-1.1/musket -k 90 600000000 -p 1000 -zlib 9 -ino…

Continue Reading Reference-based alignment using MUSKET

(ERR): bowtie2-align exited with value 13

bowtie2 – (ERR): bowtie2-align exited with value 13 1 I am trying to run bowtie2. but following error are occuring everytime bowtie2 –very-fast-local -x bowtie -q -1 R1.fastq -2 R2.fastq -s aligned.sam Saw ASCII character 10 but expected 33-based Phred qual. terminate called after throwing an instance of ‘int’ Aborted…

Continue Reading (ERR): bowtie2-align exited with value 13

Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

Continue Reading Postdoc / Research Scientist in Bioinformatics and Computational Genomics