Category: BAM

Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

Akbari MT, Izadi P, Izadyar M, Kyriacou K, Kleanthous M (2008) Molecular basis of thalassemia intermedia in Iran. Hemoglobin 32:462–470 CAS  Article  Google Scholar  Al-Allawi NA, Jubrael JM, Hughson M (2006) Molecular characterization of β-thalassemia in the Dohuk region of Iraq. Hemoglobin 30:479–486 CAS  Article  Google Scholar  Alibakhshi R, Kianishirazi…

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Empty output from UMItools dedup after fastp processing

Empty output from UMItools dedup after fastp processing 0 Hello, I have been running into an interesting error during my sequencing analysis.We have a paired-end library with UMIs on both ends of the fragments, 6 nts each, for a total of 12 nt.Now, I have been using fastp for preprocessing…

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HsMetricCollector (gatk 4.0.5.0 API)

HsMetricCollector (gatk 4.0.5.0 API) JavaScript is disabled on your browser. public class HsMetricCollector extends TargetMetricsCollector<HsMetrics> Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of target intervals and a list of bait intervals. Can be invoked either on an entire iterator of SAMRecords…

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ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files

GitHub – ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time About Wrapper script for a GenePattern module to create a velocity compatible loom file…

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Print

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CrossMap issues changing genome version

CrossMap issues changing genome version 0 I installed CrossMap for conversion of bam, bed, gtf files from one version to another. I use GENCODE so I need to make the files compatible with UCSC browser. I am running into two issues with this tool… If I use following command to…

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FASTQ to VCF pipeline question

FASTQ to VCF pipeline question 0 Hello all, I am new with programming within bioinformatics and long story short, I’m practicing writing pipeline scripts starting with the fastq to VCF pipeline. I am basically at the point where I went from fastq to sorted-bam files, and as I went to…

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bcftools mpileup before bcftools call

bcftools mpileup before bcftools call 1 I want to variant call using bcftools call. However, when researching, I see a lot of people running bcftools mpileup before doing the actual variant calling with call. For example (from here): bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf…

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Freebayes for creating VCF : meaning of QUAL

Freebayes for creating VCF : meaning of QUAL 1 Hi, I have 10 sorted Bam files 5 Male and 5 Female. I used Freebayes to create vcf files separately and then merged all 10 together. (ploidy 8) The commands I used: freebayes -f $REF -p 8 $SORTED_BAM > $OUTPUT (for…

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Error due to Sam to Bam and Indexing using picard

Error due to Sam to Bam and Indexing using picard 0 Hii all, I ran the following command: picard SortSam -I 10100123749_NIKEC.bam -O 10100123749.bam –SORT_ORDER coordinate –MAX_RECORDS_IN_RAM 1500000 –VALIDATION_STRINGENCY LENIENT But I am getting this error: 18:09:18.048 INFO NativeLibraryLoader – Loading libgkl_compression.so from jar:file:/home/mdrcubuntu/anaconda3/envs/smruti/share/picard-2.26.3-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Oct 18 18:09:18 IST 2021]…

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How to call variant minimum 3 read coverage to make consensus?

How to call variant minimum 3 read coverage to make consensus? 0 I have a query regarding consensus sequence assembly where reference bases are replaced with variants with a minimum of 3 read depths, using bcftools using the below command. bcftools mpileup -f ref.fasta mapped.bam | bcftools call -c |…

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BamIndexValidator.IndexValidationStringency – htsjdk 2.2.2 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.2.2 javadoc.io/doc/com.github.samtools/htsjdk/2.2.2 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.2.2/package-list Read more here: Source link

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My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening?

My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening? 0 The binding matrix’s peak intervals (all of them) have a width =1 bp. I have set summit=False, summit=0, summit=True. All these parameters return 1 bp width. In fact,…

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What is bigwig file?

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

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eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer’s disease mouse model

eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer’s disease mouse model 2 Hi I am a beginner to prepare eQTL analysis using mouse model for alzheimer’s disease. Is it possible to conduct eQTL analysis using ONLY brain RNA-seq data derived from 5XFAD or 3xtg mouse (The Jackson…

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correlation analysis

correlation analysis 0 Hello everyone, I have two datasets. One is normalised_counts.txt which is the results of deseq2 analysis and the other is a predixcan file which have counts for each gene for all the chromosomes. I have to do Pearson correlation to figure out how many genes in our…

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MethylDackel Error running on HPC server

Hello, I am trying to analyze data for RRBS (reduced representation bisulfite sequencing) and want to use BWA-METH for alignment. I also ran Bismark, but bismark output only shows mapping efficiency of 33.8% while BWA-METH shows 99.8% mapping efficiency (paired-end). So, I converted .sam to .bam with samtools and tried…

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Question about MACS2 genome size (other organism)

Question about MACS2 genome size (other organism) 1 Hi, I’m using MACS3 to call peak with chip-seq data from Chinese hamster ovary(CHO) cells. When running the command callpeak, macs3 callpeak -t sample.bam -c Input.bam -n output -f BAM –outdir ../5.BEDfile/ -g hs -B -q 0.01 what should I type at…

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Mapping SRA files without unpacking?

Mapping SRA files without unpacking? 1 Hi, Is it possible to submit SRA files for alignment directly to short read aligners like Bowtie, avoiding the intermediate step of unpacking data to fastq? Thanks! alignment Bowtie SRA sequencing • 35 views As of version 2.3.5 bowtie2 now supports aligning SRA reads….

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Rsubread FeatureCounts return 0.0% assigned

Using featureCounts in the Rsubread package I am getting 0 annotations. I started from raw sequencing data and the Refseq genome and Refseq Genomic GTF files downloaded from here: www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/ through the download assembly button on the side. I had the top option to RefSeq for both downloads and chose…

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Output file from samtools index is empty

Output file from samtools index is empty 0 Hello, I haven’t been able to find anything related to this question. For some strange reason after indexing .BAM file the output .BAI file is empty. No error message is shown, neither the output itself is empty (the file is created after…

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Count number of unique alignments to each chromosome from sam file

Count number of unique alignments to each chromosome from sam file 0 Hi, I want to count the number of unique reads aligned to each chromosome after mapping to the genome. I don’t mind if something is multimapped, say if read A maps to both chr3 and chr6 that is…

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Feat/support passing index files – githubmemory

v1.10 brought about the new -X option (-X include customized index file), to samtools. github.com/samtools/samtools/pull/978 Is it possible to request for tabix/bcftools/etc? Use case would be for passing in signed s3 urls into all of the various tools. e.g. tabix <signed_vcf_url> -X <signed_vcf_tbi_url> chr2 bcftools view <signed_vcf_url> -X <signed_vcf_tbi_url> chr2…

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paired reads have different names BWA MEM after samtools bam > fastq

paired reads have different names BWA MEM after samtools bam > fastq 0 I have used bwa mem to align to a host genome and output the unmapped reads. I have then sorted this resulting BAM and split into pairs fastq files. Whya fter sorting the BAM file am I…

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mapping long-reads to a reference library

mapping long-reads to a reference library 1 Hi, I have long, pacbio, reads and I have a reference library of only repeats, I want to map the long reads on the repeats library using bwa mem, is this command correct? bwa index mmm.pacbio.fastq.gz bwa mem mmm.pacbio.fastq.gz repeat-library.fasta | samtools sort…

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How can I be sure that raw read counts are well processed from fastq files?

How can I be sure that raw read counts are well processed from fastq files? 0 Hi. I’m new in bioinformatics and try to process fastq files for getting raw read count matrix. I downloaded fastq files from www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63452 I used fasterq -dump to download fastq files from SRR Aligned…

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GATK multiple files run error /usr/bin/bash: gatk: command not found

GATK multiple files run error /usr/bin/bash: gatk: command not found 0 Hello I’m using ls *.sorted_markduplicates.bam | parallel –progress –eta -j 3 ‘gatk BaseRecalibrator -I {} -R ../0.Reference/CH-PICR.fasta -O {.}.recal.bam’ to run multiple Bam files. But an error has occurred like this: Computer:jobs running/jobs completed/%of started jobs/Average seconds to complete…

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How do I compare reads between two bam file?

How do I compare reads between two bam file? 1 I would like to find reads in one bam files which are not in a second bam file. Is there an easy way to do this? My way for now is: sort both bam files by read name extract read…

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Paired end reads not properly aligning in Rsubread align

Paired end reads not properly aligning in Rsubread align 1 Hi all, I am trying to use Rsubread to align paired end RNAseq data to a mouse genome index that I built with the bulidindex function in Rsubread. I then used the command below to try to align my sequences…

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replace low quality bases with “N”

Bam file: replace low quality bases with “N” 1 Hello, is there any way to remove low quality score bases from bam files, leaving the space blank or replaced with a filler character (i.e. Ns)? I have mapped my sequencing reads, and adjusted the base quality scores (using mapDamage, which…

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Confused by MACS2 –scale-to option

Confused by MACS2 –scale-to option 1 Hi all, Quick Q regarding MACS2. The manual states that the –scale-to option serves to “scale the larger sample up to the smaller sample” or vice-versa. What exactly does it mean by this? Is this scaling only applied when multiple samples/reps are given? Or…

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Splitted sorted BAM files with samtools

Splitted sorted BAM files with samtools 1 Hello. I’m trying to use the command “sort” of samtools (ex: samtools sort alignment.bam -o alignment.sorted.bam), but for some reason, instead of generating one single sorted file (ex: alignment.sorted.bam) it generates many files (ex: alignment.sorted.bam.0000.bam, alignment.sorted.bam.0001.bam, alignment.sorted.bam.0002.bam, …, alignment.sorted.bam.0020.bam). The odd thing is…

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SAMtools markdup and insert size in Qualimap

I am using Qualimap to do some Quality Control (QC) of my bowtie2 alignment and also to compare QC reports when I mark duplicates in the BAM file using samtools markdup. While comparing these reports, I noticed a difference in the insert sizes that Qualimap gives. For example: One of…

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Bioinformatics Analyst – New York

POSITION RESPONSIBILITIES: The person will:Utilize existing pipelines to process and analyze high-throughput sequencing data, including bisulfite sequencing data.Manage, organize all bioinformatics sequencing data in the lab. Including papillomavirus sequence, microbiome data, both 16S and other, and human genomic dataConstruct phylogenic treesThe individual will be responsible for downloading large Fastq, BAM…

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Inflammation mtdna transcription replication mitochondrial biogenesis shirt

Product Description ?????????? ?????? ???? ???????? ???????? ?????????????????? ?????? ?????? ?????? ?????? ?????? ?? ???????????? ???????????? ???? ????????????. Ask ?????????????????? ???? ?????????? falling ???? ?????? ?????????? ???? ?????? ?????????? ????????????, ?????????????? ????s Cruzy ?????? ???????? ????????????????????????????????Lying Biden Surrender and Thief’Needs to be held accountable for ALL his Failures Afghanistan. Spent…

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Back-filling missing genotypes in merged VCF

Back-filling missing genotypes in merged VCF 2 Is there a good way to distinguish ./. from 0/0 in a merged vcf? For example, a tool that goes back to the bam files for missing genotypes and checks if it’s homozygous reference or a NO CALL? I would imagine this would…

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Variants in untargeted genes identified after atrgeted exome sequencing analysis

Variants in untargeted genes identified after atrgeted exome sequencing analysis 0 Hi, I recently analyzed some targeted exome sequencing samples, which were provided to us by our collaborators, for which I do not possess the target gene list. Upon analysis, I am informed that some of the genes – whose…

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Account Rep for BioBam Bioinformatics Staffing Clients

Job Description Posted October 12, 2021 Candidate must possess at least Graduate / Undergraduate of Account Rep or related course.Preferably with working experience in the related field of Customer Service is required for this position.Proven Account Rep experience.A strong portfolio of illustrations or other Account RepFamiliarity with software and technologies…

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Bioconductor – esATAC

DOI: 10.18129/B9.bioc.esATAC     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…

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sam2tsv listing incorrect reference sequence & positions

Duplicate of: github.com/lindenb/jvarkit/issues/190 Hi can anyone help me resolve the issue I’m having with sam2tsv. It is a nifty piece of software but I have been encountering issues with it regarding the numbering of nucleotides it shows for the reference sequence. Here’s what sam2tsv tells me: The nucleotide string marked…

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Aligning multiple fastq files with genome in one script/one line with STAR

Hi there! This is probably a VERY basic question but I don’t have the best terminal skills so I’m struggling a little. I want to apply what I wrote below for all my fastq scripts without doing a for loop or manually writing the code for each (ideally they all…

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Replacing BAM with CRAM Files

Replacing BAM with CRAM Files 0 I’m starting to explore mapped sequence data formats. Specifically the possibility of replacing bam files with cram files, as bam and/or ubam files are generally quite heavy. Thus can affect transfer and computational times used in my linux systems. However I wanted to know…

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SAM Validation Error with CleanSam (Aligment start must be

SAM Validation Error with CleanSam (Aligment start must be <= reference seq length) 0 I ran several bam files through a pipeline with CleanSam, SortSam, and MarkDuplicates without a problem. However, one of the input files gave me the following error with CleanSam: ERROR: Record 2106053, Read name A00187:414:HMYCYDSXY:3:1426:13367:11083, Alignment…

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extract gene sequence from multiple bam files in order to do Ka/Ks test

extract gene sequence from multiple bam files in order to do Ka/Ks test 0 Hello, I have a dataset of RNA bulk rna-seq (single-end), mapped with hisat2 and now I want to extract the sequences of some genes of my interest in order to run a Ka/Ks test for them…

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kallisto genomebam error

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. This is the code that I am using kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o $FOLDER -t 12 –genomebam -g Homo_sapiens.GRCh38.100.gtf.gz -c hg38.chrom.sizes_clean_tab.txt –rf-stranded ${FILES[$i]} ${FILES[$i+1]} My chromosome file looks like that, tabbed and…

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Comparison of sequencing data processing pipelines and application to underrepresented African human populations | BMC Bioinformatics

Literature survey We reviewed the processing pipelines of 29 HTS studies, 23 of which focus on human populations and six on other mammals (listed in Table 1). Table 1 List of studies included in the literature survey We summarized the information for some processing steps in Table 2 (see Additional…

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samtool sort

samtool sort 0 my command :bowtie2 -x Guy11 -1 Guy11_FDSW210137750-1r_1.clean.fq.gz -2 Guy11_FDSW210137750-1r_2.clean.fq.gz | samtools sort -O bam -@ 5 -o Guy11.bam and then it got error sort: invalid option — ‘O’ open: No such file or directory [bam_sort_core] fail to open file bam Can people help me ? genomics analysis…

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How to assemble read with a minimum 2 coverage per site

How to assemble read with a minimum 2 coverage per site 0 Hi, I have a query regarding read assembly I have a bam file I made a consensus sequence but I want to make a consensus sequence with a minimum of 2 coverage per site instead of full coverage…

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I Discovered A New Sister Brother Through Ancestry Com Gedmatch The Fact About download mp3 That No One Is Suggesting Mp3 Download

I Discovered A New Sister Brother Through Ancestry Com Gedmatch Official Video Date: 2020-07-25 16:22:47, The Berry Chronicles I Discovered A New Sister Brother Through Ancestry Com Gedmatch, YouTubes music destination showcasing leading tracks and common hits from various genres. This channel was created routinely by YouTubes movie disco. If…

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FGFR2 inhibitors in intrahepatic cholangiocarcinoma

Massimiliano Salati,1,2 Francesco Caputo,1 Cinzia Baldessari,1 Pietro Carotenuto,3 Marco Messina,4 Stefania Caramaschi,5 Massimo Dominici,1 Luca Reggiani Bonetti5 1Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy; 2PhD Program Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Modena, Italy; 3Department of Genomics, Telethon Institute of Genetics and…

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Twist Bioscience Staff Bioinformatics Engineer, Biopharma

Twist Biopharma is seeking a Bioinformatics Engineer to develop and integrate workflows, analyses, and computational tools involved in the production and research of antibodies and proteins. While you have a broad interest in biotech and related scientific technologies, you also understand that computer science resources must be utilized to reach…

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kallisto genomebam not showing reads on igv

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. After producing and loading the pseudoalignment bam to the igv, it is empty. This is my initial command: kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o pseudo -t 10 –genomebam -g Homo_sapiens.GRCh38.100.gtf -c hg38.chrom.sizes R1.fastq.gz.trim_1.fq.gz…

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Genetic Factors Affecting Precision Pain Medicine

Introduction The overarching definition of precision pain medicine is that diagnosis and treatment can be customized to an individual’s specific risk profile.1,2 At its most basic, the ideology is based on using all available patient-level data to target therapies for that individual with regard to prediction, prevention, diagnosis, and treatment…

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Bioinformatics Scientist Job Opening in Huntsville, AL at Discovery Life Sciences

Discovery Life Sciences are the Biospecimen and Biomarker Specialists™ serving thousands of scientists across the U.S. and around the world. We’re looking for a standout Bioinforatics Scientist for the HudsonAlpha Discovery sequencing lab in Huntsville, Alabama. The Bioinformatics Scientist contributes to our mission by taking lab-generated data and creating computational…

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DiffBind spike-in normalisation with varying amounts of spike-in chromatin

DiffBind spike-in normalisation with varying amounts of spike-in chromatin 0 Hi there! I am currently using DiffBind v3.2.7 to analyse some ChIP-seq data for RNA Polymerase III (RNAPIII). We have Drosophila spike-in chromatin in the samples that I would like to use in DiffBind to normalise the data. The problem…

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Worldwide AI Training Dataset Industry to 2028 – Featuring Appen, Cogito Tech and Scale AI Among Others

DUBLIN, October 07, 2021–(BUSINESS WIRE)–The “AI Training Dataset Market Size, Share & Trends Analysis Report By Type (Text, Image/Video, Audio), By Vertical (IT, Automotive, Government, Healthcare, BFSI), By Region, And Segment Forecasts, 2021 – 2028” report has been added to ResearchAndMarkets.com‘s offering. The global AI training dataset market size is…

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Individual donor strains show no association between fecal microbiota transplantation and successful melanoma immunotherapy

30% and average depth> 3.5). Credit: DOI: 10.1186 / s12866-021-02312-0″ width =”800″ height =”530″/> WSS score from FMT using a single donor / recipient pair. Davar et al. The WSS score was determined by comparing the donor sample with the sample of all available pairs of recipients using the data…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

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Index of /examples/archive/bioinfo/samtools

Index of /examples/archive/bioinfo/samtools Samtools/BCFtools/HTSlib Introduction and Notes Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlib A C library for reading/writing high-throughput sequencing data…

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How to obtain a protein abundance profile based on a BAM file created using bowtie2 (alignment performed with nucleotide alignment)?

How to obtain a protein abundance profile based on a BAM file created using bowtie2 (alignment performed with nucleotide alignment)? 0 I have a set of metatranscriptomics sequence samples. Let’s say the following sample fastq file is what I have. I would like to map these reads to a bacterial…

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

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chimeric vs unaligned reads

Forum:chimeric vs unaligned reads 0 Hello, I’m trying to obtain the chemic alignments from a BAM file that originally was generated by STAR and that only has a list of unaligned reads at the end of the file (so no SA tag). If I convert that BAM file back into…

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Individual donor strains do not show link between fecal microbe transplantation and successful melanoma immunotherapy – News

Fecal-dominant donor microbes in the recipient patients after fecal microbe transplantation did not correlate with response to anti-PD-1 therapy. Fecal-dominant donor microbes in the recipient patients after fecal microbe transplantation did not correlate with response to anti-PD-1 therapy.The mix of microbes in the gut can shape a person’s immune response….

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variants only found on inversion reads in IGV

Forum:variants only found on inversion reads in IGV 0 Hi, I used GATK germline variant calling pipeline to call short variants on paired end fastq files. After got the final analysis ready vcf, applied some extra filters, I inspected bam files in IGV for those variants of interest and found…

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Cenozoic climatic changes drive evolution and dispersal of coastal benthic foraminifera in the Southern Ocean

1. Thomson, M. R. A. Geological and palaeoenvironmental history of the Scotia Sea region as a basis for biological interpretation. Deep Sea Res. II 51, 1467–1487 (2004). Article  ADS  Google Scholar  2. Maldonado, A. et al. A model of oceanic development by ridge jumping: Opening of the Scotia Sea. Glob….

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TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM).

TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM). 0 I ran TPMCalculator on my RNA-seq data. This was my first time using this package. It seemed to have done without any problems, but I realized that counts of some genes are zero. I performed DEG analysis…

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NIH director Francis Collins to step down by end of year

NIH Director Dr. Francis Collins and Dr. Luciana Borio, a member of President-elect Joe Biden’s coronavirus task force speak on a COVID-19 panel Before being selected to join the task force by Biden, Borio worked as vice president of technical staff at the In-Q-Tel strategic investment firm. Until last year,…

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Francis Collins Steps Down as NIH Director after 12 Years

Francis S. Collins, MD, PhD, will end the longest tenure of any NIH director—12 years straddling the administrations of three U.S. presidents—when he steps down from the agency’s helm at year’s end. [NIH] Francis S. Collins, MD, PhD, will end the longest tenure of any NIH director—12 years straddling the…

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Statement by President Joe Biden on Dr. Francis Collins Stepping Down as Director of the National Institutes of Health

Dr. Francis Collins is one of the most important scientists of our time. During the course of his extraordinary three-decade career at the National Institutes of Health, the NIH, and the world’s preeminent medical research organization, he helped finish the sequencing and mapping of the human genome to unlock the mysteries of our DNA, which earned him the Presidential Medal of…

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Genome-wide heterozygosity

Genome-wide heterozygosity 0 Heys, I want to calculate genome-wide heterozygosity for a couple of samples I have. I have been looking in internet but I just find theoretical definitions of how you should do it, rather than practical examples. Is there any software or custom batch script already optimized? I…

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Extracting exon level read coverage of a specific gene

HTSeq – Extracting exon level read coverage of a specific gene 1 Dear all, I am trying to quantify RNASeq reads at the “exon level” using HTSeq. To achieve a quantitative exon comparison. I am using ENCODE mouse data which is Illumina reads alligned to GENCODE M27 (GRCm39) using STAR…

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How to obtain a segmentation file from Control-FREEC output to use with GISTIC

ps. sorry if my english is not too good, it is not my native language XD No te preocupes – tu inglés es excelente. —————— The main input that you require for GISTIC is the segmentation file, which should have: (1) Sample (sample name) (2) Chromosome (chromosome number) (3) Start…

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Identify Mapped reads and Unmaped Mate pairs

Identify Mapped reads and Unmaped Mate pairs 0 Hey, I have a sorted bam file which i got by mapping with reference. I want to identify two things from this bam file. How many reads mapped to each gene/contig in my bam file. As this was paired-end data, i want…

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Medical Coding Jobs Bsc Msc M.Phil Biochemistry Biotech Bioinformatics at I skills Medical Coding Solutions India

Job Description IskillsSolutions HR Nandhini 7358407557(whatsapp) [email protected] Job Description: Position: Medical Coder. . Medical Coding is the process of converting patient health information into alpha numeric codes. Coders take medical reports from doctors, which may include a patients condition, the doctors diagnosis, a prescription, and whatever procedures the doctor or…

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0 + 0 mapped when used flagstat

0 + 0 mapped when used flagstat 1 I’ve downloaded bam files from ENA, and tried samtools flagstat to confirm mapping. But the result was like this. How do I interpret this? Should I download fastq files? Thanks mapping RNA-seq • 23 views You may have downloaded unaligned BAM (uBAM)…

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SamQL: a structured query language and filtering tool for the SAM/BAM file format | BMC Bioinformatics

Our primary aim building SamQL was flexibility and high expressivity for complex queries, similar to classic SQL. Table 1 compares the expressivity of SamQL for a relatively complex query against other widely used tools such as SAMtools, Sambamba, and naive Bash. SamQL maintains consistency on complex queries involving coordinates. However,…

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IGV deletion insert size

IGV deletion insert size 0 Hi, I am trying to extract variant reads for deletion (large SVs) from DNA-seq bam files. In IGV, variant reads for deletions are labelled in red (insert size larger than expected): IGV link. I am currently using the pysam package to parse bam files. I…

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Using samtools to read a bam file

Using samtools to read a bam file 0 Hi all. I am trying to extract some information (please see below) from a bam file using samtools. Given my lack of experience, I am struggling. 1.) Total reads aligned on the forward strand 2.) Total reads aligned on the reverse strand…

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What to Know About the 2021 Nobel Prizes

Nobel Prize season is upon us once again. Every October, committees in Sweden and Norway name laureates in a variety of prizes in the sciences, literature and economics, as well as peace work. In total, six prizes will be awarded. Like everything else, the Nobels are making adjustments for the…

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Research Assistant in Genomics / Bioinformatics Jobs at Nutrition Technologies , Singapore

Less than a year of experience Important Information Make sure you’re applying to a legit company by checking their website and job posts. Job description Research Assistant in Genomics / Bioinformatics Nutrition Technologies Nutrition Technologies is an innovative company producing insects as a sustainable protein source for the animal feed…

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KEGG ENZYME: 6.3.2.6

Entry EC 6.3.2.6                  Enzyme                                  Name phosphoribosylaminoimidazolesuccinocarboxamide synthase;phosphoribosylaminoimidazole-succinocarboxamide synthetase;PurC;SAICAR synthetase;4-(N-succinocarboxamide)-5-aminoimidazole synthetase;4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase;SAICARs;phosphoribosylaminoimidazolesuccinocarboxamide synthetase;5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase Class Ligases;Forming carbon-nitrogen bonds;Acid-D-amino-acid ligases (peptide synthases)BRITE hierarchy Sysname 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming) Reaction(IUBMB) ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate [RN:R04591] Reaction(KEGG) Substrate ATP [CPD:C00002]; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate [CPD:C04751]; L-aspartate [CPD:C00049] Product ADP [CPD:C00008]; phosphate…

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Analysis of cf-mtDNA and cf-nDNA fragment size distribution using different isolation methods in BV-2 cell supernatant of starvation-induced autophagy

Available online 30 September 2021, 119147 doi.org/10.1016/j.bbamcr.2021.119147Get rights and content Highlights • Autophagy-associated cfDNA could be visualized as an oligonucleosomal DNA ladder pattern • Autophagy-associated cf-mtDNA and cf-nDNA were both highly enriched in <mono-nucleosomes fragments • Autophagy-associated cf-mtDNA and cf-nDNA showed no significant differences in the relative percentages for <mono,…

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FeatureCounts output .txt file not tab delimited

FeatureCounts output .txt file not tab delimited 1 Hi all, I ran the unix version of featureCounts on ChIPseq data using the following script: featureCounts -F SAF -p -O -T 8 -a $MACS2/All_samples_peaks.saf -o $FEATURECOUNTS/All_samples_counts.txt $BAM/*.dedup.q30.bam which ran successfully, no issues in the log or in the txt summary file….

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Is it okay to convert bam files to fastq and getting seqkit results?

Is it okay to convert bam files to fastq and getting seqkit results? 0 I’m sorry if this is a non-sense question but I am a rookie and although I searched about this I couldn’t find any decent answer. I had the fastq files but they somehow became corrupted. I…

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Subsampling Bam File With Samtools

Subsampling Bam File With Samtools 2 Hi, I am trying to subsample from a bam file using the samtools view -s command. This is working when sampling 50% or lower (-s 42.50, 42 being the seed), but anything higher fails (returns an empty file). He are the exact commands i…

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How to align incomplete pairs and singled end reads?

How to align incomplete pairs and singled end reads? 0 Hi everyone, I converted bam files to fastq files to realign them with BWA. For some bam files, I get single end read files and files with incomplete pairs. I used the tool bam2fastq by biobambam2 which states single end…

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KEGG ENZYME: 2.7.1.90

Entry EC 2.7.1.90                 Enzyme                                  Name diphosphate—fructose-6-phosphate 1-phosphotransferase;6-phosphofructokinase (pyrophosphate);pyrophosphate-fructose 6-phosphate 1-phosphotransferase;inorganic pyrophosphate-dependent phosphofructokinase;inorganic pyrophosphate-phosphofructokinase;pyrophosphate-dependent phosphofructo-1-kinase;pyrophosphate-fructose 6-phosphate phosphotransferase Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with an alcohol group as acceptorBRITE hierarchy Sysname diphosphate:D-fructose-6-phosphate 1-phosphotransferase Reaction(IUBMB) diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate [RN:R00764] Reaction(KEGG) Substrate diphosphate [CPD:C00013]; D-fructose 6-phosphate [CPD:C00085] Product phosphate [CPD:C00009]; D-fructose…

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Will DNA sequencing for every newborn become a reality in future?

Will DNA sequencing for every newborn become a reality in future? Will DNA sequencing for every newborn become a reality in future?  Science: DNA sequencing for every newborn will be the future direction of development!  In basic biology research, and in many application fields, such as diagnosis, biotechnology, forensic biology, and…

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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia

Study design and data collection We performed a cross-sectional, multisite study in 11 districts along Ethiopia’s borders with Eritrea, Sudan and South Sudan, located within three of its nine administrative regions. On average, ten health facilities were selected from each district, including four districts of Amhara Region (northwest Ethiopia), six…

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VGEA: an RNA viral assembly toolkit

This article was originally published here PeerJ. 2021 Sep 6;9:e12129. doi: 10.7717/peerj.12129. eCollection 2021. ABSTRACT Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology,…

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rs2507799 was found to be linked with increased risk for IS

Introduction Ischemic stroke (IS) is caused by the sudden loss of blood circulation to an area of the brain that causes injury to neurological function and represents a major cause of global disability and mortality.1 IS is known to be a heterogeneous and multifactorial disease. Genetic factors, particularly those involving…

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Error message running GeMoMa

Error message running GeMoMa 0 I am trying to run GeMoMa for gene annotation using RNA-seq evidence. java -jar -Xms25G -Xmx50G GeMoMa-1.6.1.jar CLI GeMoMaPipeline t=target.fasta s=own a=ref-annotation.gff g=ref.fa outdir=test r=MAPPED ERE.s=FR_UNSTRANDED ERE.m=target-accepted_hits.bam ERE.v=SILENT ERE.c=true tblastn=true Extractor.p=true Extractor.r=true Extractor.s=true Extractor.f=true AnnotationFinalizer.u=YES AnnotationFinalizer.r=NO p=true pc=true pgr=true However, I am getting this error…

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Splice aware vs splice unaware aligners?

Splice aware vs splice unaware aligners? 2 Hello, I would like a clear and simple answer on the difference of splice aware / splice unaware aligners. There is a discussion that @dfernan generated but for me the definition is not very clear. Can you help me please. 😀 aware unaware…

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Blood Derived Normal RNA_seq samples TCGA

Blood Derived Normal RNA_seq samples TCGA 3 Hi, does anyone know if there are any Blood Derived Normal samples with RNAseq data in any of the TCGA databases? I want to compare exon quantification between normal and cancer samples but I can’t find any normal blood samples. Thanks RNA-Seq TCGA…

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KEGG ENZYME: 3.6.1.22

Entry EC 3.6.1.22                 Enzyme                                  Name NAD+ diphosphatase;NPY1 (gene name);nudC (gene name);NUDT7 (gene name);nicotinamide adenine dinucleotide pyrophosphatase;NADP pyrophosphatase;NADH pyrophosphatase;NAD+ phosphohydrolase Class Hydrolases;Acting on acid anhydrides;In phosphorus-containing anhydridesBRITE hierarchy Sysname NAD(H) phosphohydrolase Reaction(IUBMB) Reaction(KEGG) Substrate Product Comment This enzyme, described from plants, animals, and bacteria, can act on both reduced and oxidized forms of…

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samtools view module output format and output file issues

output: tuple val(meta), path(“*.bam“), emit: bam path “*.version.txt“ , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? “${meta.id}${options.suffix}“ : “${meta.id}“ “”” samtools view $options.args $bam > ${prefix}.bam There could be two issues with the current code in the samtools view module: samtools view $args input.bam >…

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ATAC-seq sample normalization

What you describe seems to be a difference in signal-to-noise ratio which is not uncommon. This is where more elaborate normalization methods such as TMM from edgeR or RLE from DESeq2 come into play. See the following links on why these methods are superior. The videos talk about RNA-seq but…

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Difference in .bed target region base count and mapped base count for different tools

Difference in .bed target region base count and mapped base count for different tools 1 Hello! I was initially doing performance comparison for tools to obtain sample wide average depth of coverage. I compared several tools listed below Qualimap, GATK – DepthOfCoverage, Mosdepth and Samtools – Bedcov However, the tools…

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Using HTSeq-count for paired-end data but unsorted by SAMTOOLS

Using HTSeq-count for paired-end data but unsorted by SAMTOOLS 1 Hi there, as per thread title. If I am using HTSeq-count on paired-end mapped BAM files, but they are unsorted, and I use -s yes on the default option, is it advisable? htseq ngs • 99 views Paired-end .bam need…

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Kaggle Cryptocurrency

BlockFi – Earn Kaggle Bitcoin up to 6% by Lending Bitcoin & % on Ethereum; www.casagelsomino.it is now available in the United States; Celsius – Earn Kaggle Bitcoin up to 10% on stablecoins and % on BTC. Cryptocurrency Lending Interest Rates via DeFiRate (Also: COMP Token Price)/10(). 5 Best YouTube…

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