User: jrleary

gravatar for jrleary
jrleary130
Reputation:
130
Status:
Trusted
Location:
Lineberger Comprehensive Cancer Center
Last seen:
3 months, 2 weeks ago
Joined:
11 months, 1 week ago
Email:
j******@live.unc.edu

Lowly undergrad research assistant running bulk / single cell RNAseq and downstream analysis. Focused on pancreatic cancer. 

Posts by jrleary

<prev • 61 results • page 2 of 7 • next >
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Comment: C: How should I extract mutated genes from a VCF file?
... I'll clone the repo and give it a shot. ...
written 4 months ago by jrleary130
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Comment: C: How should I extract mutated genes from a VCF file?
... Sorry, I'm a little unsure how to describe it. I could attach a screenshot of the file while viewing it with `less`, but I'm not sure how helpful that would be. Running `head ${sample}.vcf` returns: ``` ##fileformat=VCFv4.2 ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FIL ...
written 4 months ago by jrleary130
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How should I extract mutated genes from a VCF file?
... I've written a new pipeline for my lab to process and call variants on whole exome sequencing data, built around `bwa-mem`, `samtools`, `Picard`, and `GATK`. The variant calling is done using `Mutect2`, and I've filtered and annotated the SNP/indel calls using `FilterMutect2` and `Funcotator`. Whole ...
exome gatk wes written 4 months ago by jrleary130
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Comment: C: How much RAM / how many CPUs should I allocate for Mutect2?
... According to [this post on the GATK forums][1], `Mutect2` does not support multithreading. With 100G of RAM, it took 4.35 hours to process the first chromosome. This is using `gatk v4.1.2`, which supposedly has "significant speed improvements." [1]: https://gatkforums.broadinstitute.org/gatk/di ...
written 4 months ago by jrleary130
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How much RAM / how many CPUs should I allocate for Mutect2?
... I'm running `Mutect2` on some WES data. The `.bam` file is 4.7G, and I'm comparing it against the hg38 reference genome. I allocated 8 CPUs and 90G of memory using slurm, but progress has been very slow. If I wanted the job to complete for single sample within ~24 hours, what sort of CPU and memory ...
wes written 4 months ago by jrleary130 • updated 4 months ago by steve2.6k
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Comment: C: Picard CollectSequencingArtifactMetrics error
... This worked; I would add though that to use the `-R` flag, one needs to enclose the string in single quotes, like `'@RG\tID:$samplename'` instead of double quotes, like `"@RG\tID:$samplename"`, otherwise it will not work. ...
written 4 months ago by jrleary130
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Comment: C: Picard CollectSequencingArtifactMetrics error
... Thank you so much; I am a little bit confused about what string I should use as the read group argument? Can it be an arbitrary name or does it need to follow a certain naming convention? ...
written 5 months ago by jrleary130
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Comment: C: Picard CollectSequencingArtifactMetrics error
... Specified them at what step? I ran `samtools view -H | grep '^@RG'` and got nothing in return, which I'm guessing means I failed to specify them at some point when I was supposed to. EDIT: might this have something to do with how I combined the R[1-2]_L001.fastq & R[1-2]_L002.fastq files? I us ...
written 5 months ago by jrleary130
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Comment: C: Picard CollectSequencingArtifactMetrics error
... So I ran `picard ValidateSamFile` and did receive the error: ``` ERROR:MISSING_READ_GROUP ``` The .bam file was generated automatically as output from `bwa mem`, first in .sam format and then converted to .bam using `picard SamFormatConverter`. So, I'm guessing that I didn't declare the read group ...
written 5 months ago by jrleary130
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Comment: C: Picard CollectSequencingArtifactMetrics error
... Same error, unfortunately. ...
written 5 months ago by jrleary130

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