Tag: STAR

Introduction UCL-BLIC/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data, modified to add kallisto. The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) as well as kallisto abundance files, and performs extensive quality-control on the…

Stephen Sondheim, the legendary Broadway songwriter, has died at his home in Connecticut at the age of 91, according to The New York Times. The prolific composer and lyricist was the creative force behind some 20 musicals starting in 1954 — including West Side Story (lyrics), A Funny Thing Happened…

Stephen Sondheim, the legendary Broadway songwriter, has died at his home in Connecticut at the age of 91, according to The New York Times. The prolific composer and lyricist was the creative force behind some 20 musicals starting in 1954 — including West Side Story (lyrics), A Funny Thing Happened…

pytorch-openpose pytorch implementation of openpose including Body and Hand Pose Estimation, and the pytorch model is directly converted from openpose caffemodel by caffemodel2pytorch. You could implement face keypoint detection in the same way if you are interested in. Pay attention to that the face keypoint detector was trained using the…

STAR alignment in a full directory 0 Hi! I’m working with STAR and I would like to align multiple file, but separately. I have file paires like these two: Dros_01_S48_L001_R1_001.fastq.gz Dros_01_S48_L001_R2_001.fastq.gz etc. Only the S[number] changes and the R1 and R2 in the names. I have a code, what I…

Roche will present a slew of new data at the American Society of Hematology’s (ASH) annual meeting next month, showcasing new immunotherapies, treatment combinations, novel endpoints and fixed-duration regimens from its blood disease portfolio. The company will present 90 abstracts, including 17 oral presentations. The new data, which includes results…

Stacey Dash was born in the Bronx, New York. Stacy knew that she wanted to act, and from an early age began to act professionally. She made regular appearances on The Cosby Show (1984), The Fresh Prince of Bel-Air (1990), and also St. Elsewhere (1982). At 21 she made her…

Stacey Dash was born in the Bronx, New York. Stacy knew that she wanted to act, and from an early age began to act professionally. She made regular appearances on The Cosby Show (1984), The Fresh Prince of Bel-Air (1990), and also St. Elsewhere (1982). At 21 she made her…

STAR alignment barely changes when limiting the maximum number of mismatches 0 Hello everyone. I’m working with STAR aligner to map microRNA seq samples into the whole mouse genome. While taking a look at the parameters, I noticed the parameter —outFilterMismatchNmax had as default mismatch number 10 (according to the…

FeatureCount summary in RNA_Seq analysis 0 Hi, I have a doubt about the number of reads mapped to genes in the featureCounts report. Is it possible that the number of reads mapped to genes is greater than the total number of reads? For exemple : Mapping repport : using STAR…

CNN Making some truly eyebrow-raising remarks about vaccines on Sunday, Virginia Lt. Gov.-elect Winsome Sears refused to share her vaccination status because she feels it is a “slippery slope” that will eventually lead to the disclosure of her DNA information. Sears, a rising Republican star who became both Virginia’s first…

STAR for mouse RNA-seq alignment, which parameters should I use besides the basic ones in practice? 0 Hi Currently I have pair-end mouse RNA-seq data. 3 Tissues with 17 samples/tissue. Length of the sequence is from 100bp to 150bp. My goal is to perform DEG after the alignment. This is…

STAR two -pass mode – lower alignment rate than one pass mode? 0 Hi guys, Quick question. I’ve performed a two-step alignment with STAR 2.6a. It seems my unique alignment rates are approx 1% (85%) lower when performing two pass, than the original one pass mode (86%). I thought the…

STAR two -pass mode – lower alignment rate than one pass mode? 0 Hi guys, Quick question. I’ve performed a two-step alignment with STAR 2.6a. It seems my unique alignment rates are approx 1% (85%) lower when performing two pass, than the original one pass mode (86%). I thought the…

Weird output of geneCount for STAR? 1 Hi I’m using STAR to perform alignment and my goal is to do the DEG analysis in the future. The parameter I set up as follows: Step 1: STAR –runThreadN 12 –runMode genomeGenerate –genomeDir genomedir –genomeFastaFiles ./ref/GRCm39.primary_assembly.genome.fa –sjdbGTFfile ./ref/gencode.vM27.primary_assembly.annotation.gtf –sjdbOverhang 100 Step 2:…

Weird output of geneCount for STAR? 1 Hi I’m using STAR to perform alignment and my goal is to do the DEG analysis in the future. The parameter I set up as follows: Step 1: STAR –runThreadN 12 –runMode genomeGenerate –genomeDir genomedir –genomeFastaFiles ./ref/GRCm39.primary_assembly.genome.fa –sjdbGTFfile ./ref/gencode.vM27.primary_assembly.annotation.gtf –sjdbOverhang 100 Step 2:…

Error after STAR mapping 0 Hi, I’m doing the STAR mapping, but I get the bam files with some problems.When I use the command samtools flagstat SRR7195620_2.fastq.gz_Aligned.sortedByCoord.out.bam to see the details of the bam file,it shows this: 3266075 + 0 in total (QC-passed reads + QC-failed reads) 1044500 + 0…

Using STAR for mouse RNA-seq alignment, which parameters of STAR besides the basic ones would be better to use in practice? 0 Hi Currently I have pair-end mouse RNA-seq data. 3 Tissues with 17 samples/tissue. Length of the sequence is from 100bp to 150bp. My goal is to perform DEG…

Friday Pick of the day: Bridget Riley – Painting The Line 9pm, BBC Two “She moved art on 500… no, a thousand years,” says Tracey Emin of Bridget Riley, whose sometimes dizzying line paintings made the artist a poster girl for the 1960s. Centred on Kirsty Wark’s rare interview with…

36 Student Teams from Around the Asia Pacific (APAC) Region Participated in the Six-Month Long Competition which included Training and Hands-on Challenges SINGAPORE & SUNNYVALE, Calif., November 18, 2021–(BUSINESS WIRE)–The HPC-AI Advisory Council (HPCAIAC) and National Supercomputing Centre (NSCC) Singapore today announced the university team winners of its annual HPC-AI…

Arcinas C, Tan W, Fang W, Desai TP, Teh DCS, Degirmenci U, Xu D, Foo R, Sun L (2019) Adipose circular RNAs exhibit dynamic regulation in obesity and functional role in adipogenesis. Nat Metab 1:16. doi.org/10.1038/s42255-019-0078-z CAS  Article  Google Scholar  Aronoff SL, Berkowitz K, Shreiner B, Want L (2004) Glucose…

Before You Start To install YOLOP dependencies: pip install -qr github.com/hustvl/YOLOP/blob/main/requirements.txt # install dependencies YOLOP: You Only Look Once for Panoptic driving Perception Model Description   YOLOP is an efficient multi-task network that can jointly handle three crucial tasks in autonomous driving: object detection, drivable area segmentation and lane detection….

1. Muller, H. J. The relation of recombination to mutational advance. Mutat. Res. Mol. Mech. Mutagen. 1, 2–9 (1964). Google Scholar  2. Maynard Smith, J. The Evolution of Sex (Cambridge University Press, 1978). Google Scholar  3. Avise, J. C. Clonality (Oxford University Press, 2008). Google Scholar  4. Hamilton, W. D.,…

very low mapping rate of polysome profling seq 0 when i use sequencing data from SRR7695423 frist, i use fastp to trim raw reads: fastp -i r1_fastq.gz -I r2_fastq.gz -o r1_trimmed_fastq.gz -O r2_trimmed_fastq.gz then i use STAR to align: STAR –runThreadN 20 –genomeDir index –readFilesIn r1_trimmed_fastq.gz r2_trimmed_fastq.gz –readFilesCommand ‘zcat’ –outFileNamePrefix…

very low mapping rate of polysome profling seq 0 when i use sequencing data from SRR7695423 frist, i use fastp to trim raw reads: fastp -i r1_fastq.gz -I r2_fastq.gz -o r1_trimmed_fastq.gz -O r2_trimmed_fastq.gz then i use STAR to align: STAR –runThreadN 20 –genomeDir index –readFilesIn r1_trimmed_fastq.gz r2_trimmed_fastq.gz –readFilesCommand ‘zcat’ –outFileNamePrefix…

RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, which reference genome should I download when using STAR aligner? 1 I’m trying to perform alignment using STAR for my RNA-Seq data of Lung, right ventricle (RV) and left ventricle (LV) of Mouse, I wonder which reference…

Image Recognition for Beginners using CNN in R Studio Requirement Students will need to install R and RStudio software but we have a separate lecture to help you install the same Description You’re looking for a complete Convolutional Neural Network (CNN) course that teaches you everything you need to create an Image…

Gene Ontology for the species Malus domestica 1 Hi all, I mapped my reads using STAR and have feature counts. In R, I am using edgeR, limma, and voom for differential expression analysis. I did TREAT and glmMD plot. I have the differential expression list based on Gene-ID. For gene…

Hi! I’m checking the output from gene_bodyCoverage.py using a bed file with housekeeping genes. We sequenced some samples using a polyA capture library (all in the same kit, same sequencing run), so I would expect a 3′ bias. However, the output I got was somewhat mixed – I see some…

Translator | Liangchu In this chapter, we will review the previous chapters from the perspective of the entire book, see how the seemingly independent topics discussed in this book are interdependent, and understand how researchers can combine these content to solve the problem at hand. The problem. We will also…

using rsem sample.genome.STAR.genome.bam for calculating expression 0 Hello, I have run rsem-calculate-expression on pair end sequencing. From the resulting BAM file mapped to the genome (sample.STAR.genome.bam), I would like to use that as in input to calculate expression of genes in the sample. When I try to use it as…

Significance Small nucleolar (sno)RNAs generally guide ribosomal RNA and small nuclear RNA modifications, essential events for ribosome and spliceosome biogenesis and function. Most are processed in the nucleus from lariat intronic RNAs, which are unstable byproducts of splicing. We report here that some snoRNAs are encoded within unusually stable lariats….

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STAR genomeSAindexNbases 0 Hello everyone! what is the exact meaning of the parameter genomeSAindexNbases which is used for building genome index by STAR? (the mannual says For small genomes, the parameter –genomeSAindexNbases must to be scaled down) Thanks a lot! Pei RNA-seq STAR mapping • 20 views • link 2…

Using 2i/LIF and ERCC inserted RNA cultured mouse embryonic stem cells (mESCs) as materials, using 6 different library preparation methods (CEL-seq2/C1, Drop-seq, MARS-seq, SCRB-seq, Smart-seq /C1 and Smart-seq2) prepare single-cell RNA-seq data. The difference between these methods lies in the use of unique molecular marker (UMI) sequences, which can distinguish…

Contract: 3 months Pay: $22.91/hr ONSITE Description Perform bulk differential gene (ideally microarray and RNA-seq) and enrichment analysis in the R programming language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene (limma/varianceParition dream or other R method) and single-sample…

Job Title: Bioinformatics analystLocation: Lake County, IL; 100% remoteDuration: 6 months Payrate: $24/hr on W2 DescriptionWe have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or…

image: HIBARI is the demonstration Satellite with variable shape attitude control. view more  Credit: Tokyo Institute of Technology A research team[a], led by Professor Saburo Matunaga of the Department of Mechanical Engineering, School of Engineering, Tokyo Institute of Technology (Tokyo Tech), developed a 50 kg class technology demonstration microsatellite called HIBARI…

As a part of Visual Studio 2022, Microsoft added new ways for users to personalize documents so that users can code the way they want to. These new features focus on flexibility and inclusivity for working with documents and managing tabs. Users can now color file tabs by project, a…

As part of Visual Studio 2022, Microsoft added new ways for customers to personalize paperwork in order that customers can code the way in which they would like to. These new options center of attention on flexibility and inclusivity for running with paperwork and managing tabs. Users can now colour…

How select top enriched regions from plotHeatmap outputs? 0 I used the deeptools to draw plotHeatmap for ChIP-seq peaks across an epigenome mark. Now, I would like to select top (e.g: top1000) enriched regions based on the plotHeatmap to apply Motif analysis on those regions but I am not sure…

snakemake input wildcards 0 Please, can anybody explain what the wildcards in the code below does. Also, I have come across both “*wildcards” and “wildcards”, how are they different?. In this case, does **wildcards mean wildcards.sample? def STAR_input(wildcards): if config[“PE_or_SE”] == “SE”: fq1=”analysis/trimmed_data/{sample}_R1_trimmed.fq.gz”.format(**wildcards) return fq1 elif config[“PE_or_SE”] == “PE”: fq1…

Open for discussion of Remote  We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene?ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential…

Researchers in Singapore have developed the world’s largest and highest-resolution atlas of gastric cancer. It is believed that this world’s largest analysis of gastric tumor cells will provide a launchpad for scientists to plan more effective therapies for this type of cancer. Findings from the study have shown new insights…

Northwestern University announces the winners of the 2021 international Kabiller prize and awards, which biennially recognize three top scholars — one pioneer, one young investigator and one rising star — in the field of nanoscience and nanomedicine. David Walt, the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard Medical School,…

STAR producing an empty BAM file 0 I’m trying to run STAR but I am getting an empty BAM file. Does anyone know why this is happening and how to fix it? iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN > –annotation homo_sapiens.88.gtf.gz #for context, mapstar needs the following arguments reads, genome_index, out_dir…

Very low read counts for PD1 when using STAR aligner compared to BWA 0 HI all, I am processing RNA-seq data. Initially, the company used BWA and GRCh37/hg19 as an aligner. I subsequently realigned them using STAR and GRCh38/hg38. Counts are generated using feature counts for both. Although most of…

STAR alignment issue. % of reads unmapped: too short 0 I am trying to do a star alignment of the trimmed reads. Fastqc report after cutadapt tells me that my average read length is 101. When I run star, I see that is has average input read length of 185,…

DOI: 10.18129/B9.bioc.GEM     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see GEM. GEM: fast association study for the interplay of Gene, Environment and Methylation Bioconductor version: 3.12 Tools for analyzing EWAS, methQTL and GxE genome widely. Author: Hong Pan, Joanna D Holbrook,…

STAR Index 1 Is there a way to view what version of STAR made a STAR index? I’m asking because newer STAR versions are not always compatible with older STAR versions. Thanks! STAR bam • 25 views The Log.out file generated when the index is built gives the STAR version…

1. Johnston, L. A., Prober, D. A., Edgar, B. A., Eisenman, R. N. & Gallant, P. Drosophila myc regulates cellular growth during development. Cell 98, 779–790 (1999). CAS  PubMed  Article  Google Scholar  2. Sabo, A. et al. Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature 511,…

STAR alignment error “expr: syntax error” 0 Hello, I am trying to use STAR aligner. The .err file has the following message: “expr: syntax error” The .out file is as follows: Oct 28 00:12:06 ….. started STAR run Oct 28 00:12:07 ….. loading genome Oct 28 00:12:09 ….. started mapping…

STAR- error 0 Hi. I’m trying using aligner STAR, with the follow scprit: /opt/STAR-2.7.9a/bin/Linux_x86_64/STAR –genomeDir /home/julia.nicoliello/genome_index –readFilesCommand zcat –readFilesIn /home/julia.nicoliello/fastq-files/Giselle_S13_L002_R1_001.fastq.gz /home/julia.nicoliello/fastq-files/Giselle_S13_L002_R2_001.fastq.gz –outFileNamePrefix /home/julia.nicoliello/resultado_star –outFilterType BySJout –outSAMunmapped Within –outSAMtype BAM SortedByCoordinate –outSAMattrIHstart 0 –outFilterIntronMotifs RemoveNoncanonical –runThreadN 20 –quantMode TranscriptomeSAM –outWigType bedGraph –outWigStrand Stranded But, I have error 109, with this message:…

Low mapping frequency on STAR 0 Hi all, I’ve been trying to re-map some RNA-seq fasta files to mm39 using STAR. I was told by the sequencing facility who ran the requencing for me that when they mapped the reads onto mm10 using BWA MEM their mapping frequency for each…

How should I deal with my RNAseq result with high % of mutiple aligned reads? 1 Here is one of my result from STAR alignment. As you could see, Uniquely mapped reads: 32.37% and % of reads mapped to multiple loci: 60.74% This sounds not that bad because more than…

Trouble to generate genome indexes for human RNA-seq reads in STAR 0 Hi everyone, I´m a masters student and new at bioinformatics. My research is in RNA-Seq analysis, and right now I´m having trouble to generate the genome indexes prior to the alignment in STAR. A couple minutes after lauching…

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STAR alignment speed? 1 Hello, I’m currently running some RNA-seq experiment alignments on a server with STAR. After about two hours, looking at the head of the Log.progress.out file, I am getting a result like this: My total read count for the sample is ~80,000,000 reads. Does this mean that…

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How to deal with high % of reads mapped to multiple loci on STAR? 0 Here is one of my result from STAR alignment. As you could see, Uniquely mapped reads: 32.37% and % of reads mapped to multiple loci: 60.74% This sounds not that bad because more than 90%…

Ensemble file Mus_musculus.GRCm38.dna.primary_assembly.fa.gz unzipping to incorrect contents 1 Hi All, I am trying to create a RSEM index, but am running into an issue with the genome fasta file. When I download Mus_musculus.GRCm38.dna.primary_assembly.fa.gz from ftp.ensembl, it unzips to Mus_musculus.GRCm38.dna.chromosome.1.fa and I get an error that chromosomes are missing. I am…

Low assigned alignments 0 Basecalls performed using CASAVA version v1.8.2 Trimmed reads with fastx_quality_trimmer 0.0.13 with a quality treshhold of 18 and a length of 20 Aligned with Bowtie 2.1.0 and Tophat 2.0.10 using Gencode v19 junctions Samtools 0.1.19-44428cd to make a bam, sort, index Raw counts were generated using…

Junior Bioinformatician at the Lymphoma Genomic Laboratory Open position Junior Bioinformatician at the Lymphoma Genomic Laboratory Institute of Oncology Research (IOR) Bellinzona, Switzerland www.ior.usi.ch www.ior.usi.ch The Institute of Oncology Research (IOR) in Bellinzona, Switzerland, is a rapidly evolving,leading center for basic and translational research in oncology in Europe.IOR is affiliated…

How should I align my single-end fastq file? 0 I have this RNA-seq fastq file which is SINGLE-end. However, I couldn’t figure out these fastq files are unstranded or strand-specific. I cannot even know if their orientation is forward or reversed… I ran STAR alignment with command: STAR –runThreadN 32…

Isoform Analysis: StringTie creates .tsv value that has null values for every gene id 0 Hi everyone, I am new to bioinformatics and Biostars as a whole. I am doing isoform analysis on some samples and I’ve come across a problem. The following code is what I used for StringTie….

STARaligner not recocognizing “:” Illumina Quality Score Encoding resulting in “quality string length is not equal to sequence length”error? 0 HI recently I got this fatal error from STARaligner. EXITING because of FATAL ERROR in reads input: quality string length is not equal to sequence length @A00269:556:HHTWKDRXY:1:2234:19696:18286 + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF however…

Hello, My results from cellranger and starsolo are very different. The estimated cell number of cellranger count with default parameters was 9400 while starsolo estimated 3600. I am confused by the big variation. When I check the results from cellranger, there are two big cell clusters with very high UMI…

RNA seq trimming 1 I am writing to know if 2-4 percent n content near the both ends of a sequence (RNA seq, read length:150) would be a problem and need trimming? RNA-Seq • 1.4k views It depends on the aligner that you use. If you’re using something like hisat2…

featureCounts has low successfully assigned reads 1 After finishing STAR two-step alignment, I got 62% uniquely mapped reads. But featureCounts gives me only 17% successfully aligned rate. featureCounts -T 8 -F GTF -p –countReadPairs -t exon -g gene_id -a ~/genome_ref/gencode.v38.annotation.gtf -o ~/expression/all_counts.txt *.bam I also have a look at other…

Event listing from University of Pittsburgh: Wednesday, October 20 from 1:00 PM to 3:00 PM This will be a flipped class â�� a prerecorded video and a hands-on workshop â�� which will cover the basics of command-line skills for data analysis. During this class, participants will learn how to:access Center…

Significance Proteins are the key drivers of neuronal synaptic function. The regulation of gene expression is important for the formation and modification of synapses throughout the lifespan. The complexity of dendrites and axons imposes unique challenges for protein supply at remote locations. The discovery of messenger RNAs (mRNAs) and ribosomes…

Detailed population structure of L1–4 and a hierarchical sub-lineage naming system We assembled a high-quality data set of whole genomes, antibiotic resistance phenotypes, and geographic sites of isolation for 9584 clinical Mtb samples (“Methods” section and Supplementary Data 1). Of the total, 4939 (52%) were pan-susceptible, i.e., susceptible to at least…

Germany’s Benjamin List and US-based David MacMillan yesterday won the Nobel Chemistry Prize for developing a tool to build molecules which has helped make chemistry more environmentally friendly. Their tool, which they developed independently of each other in 2000, can be used to control and accelerate chemical reactions, exerting a…

I’m not sure my Bulk RNAseq read counts extracted from fastq file are correct 1 Hi. I’m new in bioinformatics and I’m trying to extract read counts from fastq files. I used STAR alignment method with GENCODE annotation files. (I didn’t trimmed by reads because I heard that trimming is…

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In principle it is working. on gmod possessor mod. Found inside – Page 241The problem is that a postprocessing vertex for argument y in the call to Add from A is included in A’s procedure … summary information consists of the following sets , which are computed for each procedure…

Update: Fixed bumpmaps and rigging errors for all! –I did not make this addon, I’m only supporting the community by adding it to the Gmod 13 workshop.–. Go the the GMOD Textures Page. However, I feel that this pack has both more content at a higher quality than pack 1,…

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Use of aligners (preferably STAR) for read-barcode matching 0 My goal is to match a custom single cell type library with unknown barcode locations across reads but known sequences: I have made a ‘genome’ of ~70nt of each ‘read’ (17mX70nt contigs) and have aligned putative barcodes (~70kX32nt) against this. I…

samtools to count the number of reads mapped to each spike-in for each sample 0 My goal is to use STAR to create a new genome with the spike-ins listed below by combining both hg38.fa and spike-in. Once I have the genomes created, I’ll align FASTQs to this newly created…

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…

Error with indexing! STAR unable to access genome file SOS 0 I keep receiving the error: EXITING because of INPUT ERROR: could not open genomeFastaFile: – Does anyone know why this could be? The code I run: STAR –runMode genomeGenerate –genomeDir /scratch/e51/trial2/align/sequence/STARindex –genomeFastaFiles /scratch/e51/trial2/align/sequence/genome/GRCm39.ens.fa –runThreadN 12 I provide the full…

9-Oct-2021 (Sat) Wherein Halloween is creeping up Halloween Week is almost upon us, and as per tradition, you can get a Five Night Multipass! This ticket admits one person to seven parties over five nights: Sequence, Star Crash, All Hallow’s Eve, Booootie, Technolatry, So Stoked and Death Guild! (Note: one…

cellranger count output does not give all genes. 0 Dear all, I have recently started using the cellranger from 10x for scRNA-seq data, after having used my own pipeline (with STAR alignment) for smart-seq2 data, to get the count matrix for then later analyzing with Seurat or Scanpy. I have…

I am using a script to analyze a large amount of ribo-seq data, which comes from different studies. Because from different research, I use trim_galore to remove the adaptor. Use bowtie2 to remove rRNA and use STAR mapping. After mapping, I found that the mapping rate of some of the…

Photo: Francis Collins, by NIH Image Gallery, via Flickr. Dr. Francis Collins has just announced his intention to step down as Director of the U.S. National Institutes of Health. Collins made the announcement after coming under scrutiny for allegedly lying about authorizing the funding of controversial and dangerous research at the notorious virus…

There really is such a thing as too much information. Say, for instance, you’re an astronomer scanning the cosmos for black holes, or a climate scientist modeling the next century of global temperature change. After just a few days recording observations or running simulations on the most sophisticated equipment, you…

STAR-aligner: genome load in a for-loop 0 I am running multiple samples defined in files.txt. How should I load the genome correctly to avoid it being loaded for each iteration in the loop? I tried the following, but the –genomeLoad LoadAndKeep required fastq-files to be loaded, in addition to the…

SVAseq for differential transcript usage and differential splicing analysis 0 Hi, I am working with bulk RNA-seq data from ~300 samples of human healthy and diseased tissue. The data were mapped to the reference transcriptome using Salmon and were summarised to gene-level and transcript-level using tximport (LengthscaledTPM and DTUscaledTPM) functions…

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…

image: Figure 1. Research findings suggest that neoadjuvant treatment with retinoids may promote the conversion of highly aggressive mesenchymal cancer cells to less aggressive epithelial cancer cells in breast cancer. This can render breast tumours more responsive to subsequent chemotherapy and produce a durable treatment outcome. A clinical trial is underway…

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…

Job Description Bioinformatics Specialist We are inviting applications for a bioinformatics specialist position at the Genome Institute of Singapore. Successful candidate will join the research program on generating a human pangenome reference for Asian populations. The current reference (hg37/38) plays an essential role in large-scale genome sequencing analysis of human…

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…

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…

STAR bisulfite mapping 0 Hi all, I’m mapping bisulfite-treated and untreated (control) of total RNA. I expect multi-mapping to several rRNA loci (in E coli there are 7 rRNA loci, for example). When I map untreated samples to a ‘normal’ genome/transcriptome I do get multi-mapping, but when I map treated…

Researchers from the Agency for Science, Technology and Research’s (A*STAR) Genome Institute of Singapore (GIS), and Rady Children’s Institute for Genomic Medicine identified a previously unknown condition affecting children, which they discovered could be prevented by administering a drug during pregnancy. Through a worldwide collaboration, the researchers identified children from…

Job Description Job Description We are looking for a highly-motivated and skilled bioinformatics specialist to work on data analysis of patient biosamples. employing multi-omics approaches including bulk tumor next-generation sequencing (NGS), single cell RNAseq, CyTOF, and 3D spatial transcriptomics in the context of a clinical cohort of rare tumours. The…

Variants classed as definitely pathogenic in humans Among the 18 mutations of Complex 1 that are definitely pathogenic after application of the modified scoring system, 11 were found in at least one species from our dataset, and four of them occurred on the phylogenetic tree more than once (Table 1,…

Data reporting No statistical methods were used to predetermine sample size.  Data collection was performed by independent investigators. Prior to data analysis, all experiments were randomized and analysed by independent blinded observers. Analysis of human and macaque transcriptomic data Developing human and macaque brain RNA-seq data (counts file) with the…