User: gprashant17

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gprashant1740
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4 weeks, 1 day ago
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Posts by gprashant17

<prev • 12 results • page 1 of 2 • next >
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Comment: C: What are the best set of options to use while aligning using STAR?
... Thanks, I would like to separate the mapped and unmapped reads into two different SAM/BAM files and I did not notice a way to do that in the manual. Is there any other way or including the unmapped reads within the same alignment file is the only option? ...
written 18 hours ago by gprashant1740
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Comment: C: What are the best set of options to use while aligning using STAR?
... I just tried using --chimSegmentMin 20 --chimOutType WithinBAM. Most of my reads are 2*101 base pairs long and the minimum is around 40 (for one mate). I used WithinBAM option as that would allow me to use another option --peOverlapNbases, for detecting overlapping within read pairs. As this would ...
written 18 hours ago by gprashant1740
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Comment: C: What are the best tools for analyzing and identifying somatic mutations?
... Using a few of them and comparing the results would work I guess, thanks. ...
written 3 days ago by gprashant1740
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What are the best set of options to use while aligning using STAR?
... Hi, I have a tumour RNA-seq data, which I have aligned using STAR with a human reference genome, using the basic default options. However, I am confused with the variety of options (chimeric junctions, 2-pass mapping, readCounts, etc) available in the STAR manual and I would like to know which of th ...
ngs alignment star rna-seq written 3 days ago by gprashant1740 • updated 1 day ago by Charles Warden6.8k
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What are the best tools for analyzing and identifying somatic mutations?
... Hi, I am looking for tools to identify somatic mutations (SNPs, CNVs, indels, etc) from a tumour sample (RNA-seq) which has been aligned with the human reference genome using STAR. I noticed that there are many tools (MuTect, MuSE, VarDict, etc) for generating a vcf file. It looks like these tools r ...
vcf bam snp rna-seq sam written 3 days ago by gprashant1740 • updated 3 days ago by ATpoint17k
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Comment: C: Usage of Mutect2
... Since I do not have the data for any normal tissue from the same human, is there a way to skip this step? ...
written 7 days ago by gprashant1740
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Usage of Mutect2
... Hi, I have been trying to use the Mutect2 of GATK toolkit, and noticed an example usage: java -jar GenomeAnalysisTK.jar \ -T MuTect2 \ -R reference.fasta \ -I:tumor tumor.bam \ -I:normal normal.bam \ [--dbsnp dbSNP.vcf] \ [--cosmic COSMIC.vcf] \ [-L targets.in ...
gatk next-gen snp rna-seq mutect2 written 8 days ago by gprashant1740 • updated 8 days ago by MatthewP110
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Comment: C: Viewing and editing FASTQ files
... As far as I know, the BAM file which I have was generated from a different pipeline and when I try to convert to fastq, it results in a truncated file having format errors like: 1) ^B symbol is present in some places instead of breaking into a new line 2) few incomplete records 3) RNA sequence havi ...
written 11 days ago by gprashant1740
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What is Canonical/Non-canonical splicing?
... I am using STAR aligner to align an RNA-seq data with a human reference genome and I was analysing the log.final.out file. I am not sure what the following results mean: Number of splices: GT/AG Number of splices: GC/AG Number of splices: AT/AC Number of splices: Non-canonical : I understand ...
ngs alignment star rna-seq splicing written 11 days ago by gprashant1740 • updated 11 days ago by Jean-Karim Heriche19k
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Comment: C: Viewing and editing FASTQ files
... I tried this too, it starts running and shows this error finally: Invalid maximum heap size: -Xmxm Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. ...
written 13 days ago by gprashant1740

Latest awards to gprashant17

Student 3 days ago, asked a question with at least 3 up-votes. For What are the best set of options to use while aligning using STAR?

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