User: jrleary

gravatar for jrleary
jrleary160
Reputation:
160
Status:
Trusted
Location:
Lineberger Comprehensive Cancer Center
Last seen:
3 weeks ago
Joined:
1 year, 1 month 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 • 63 results • page 2 of 7 • next >
1
vote
0
answers
641
views
0
answers
Comment: C: Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
... As quickly as I asked this, I figured it out. The hidden function `CalcN` performs this: ``` nCount = colSums(x = object, slot = "counts") # nCount_RNA nFeature = colSums(x = GetAssayData(object = object, slot = "counts") > 0) # nFeatureRNA ``` ...
written 6 months ago by jrleary160
1
vote
0
answers
641
views
0
answers
Can I manually add nCount_RNA & nFeature_RNA to a converted Seurat object?
... I'm converting a `SingleCellExperiment` object to a `Seurat` object, and I'd like to be able to regress out the effect of % mitochondrial DNA when running `SCTransform` for normalization & detection of highly variable genes. However, running `as.Seurat` does not add the necessary `nCount_RNA` or ...
scrna-seq R seurat written 6 months ago by jrleary160
0
votes
0
answers
339
views
0
answers
Comment: C: How should I extract mutated genes from a VCF file?
... I'll clone the repo and give it a shot. ...
written 7 months ago by jrleary160
0
votes
0
answers
339
views
0
answers
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 ${sample}.vcf` returns: ``` ##fileformat=VCFv4.2 ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FIL ...
written 7 months ago by jrleary160
0
votes
0
answers
339
views
0
answers
How should I extract mutated genes from a VCF file?
... I've written a new pipeline for my lab to process and call variants on whole exome sequencing data, built around `bwa-mem`, `samtools`, `Picard`, and `GATK`. The variant calling is done using `Mutect2`, and I've filtered and annotated the SNP/indel calls using `FilterMutect2` and `Funcotator`. Whole ...
exome gatk wes written 7 months ago by jrleary160
0
votes
1
answer
443
views
1
answers
Comment: C: How much RAM / how many CPUs should I allocate for Mutect2?
... According to [this post on the GATK forums][1], `Mutect2` does not support multithreading. With 100G of RAM, it took 4.35 hours to process the first chromosome. This is using `gatk v4.1.2`, which supposedly has "significant speed improvements." [1]: https://gatkforums.broadinstitute.org/gatk/di ...
written 7 months ago by jrleary160
2
votes
1
answer
443
views
1
answer
How much RAM / how many CPUs should I allocate for Mutect2?
... I'm running `Mutect2` on some WES data. The `.bam` file is 4.7G, and I'm comparing it against the hg38 reference genome. I allocated 8 CPUs and 90G of memory using slurm, but progress has been very slow. If I wanted the job to complete for single sample within ~24 hours, what sort of CPU and memory ...
wes written 7 months ago by jrleary160 • updated 7 months ago by steve2.7k
0
votes
1
answer
297
views
1
answers
Comment: C: Picard CollectSequencingArtifactMetrics error
... This worked; I would add though that to use the `-R` flag, one needs to enclose the string in single quotes, like `'@RG\tID:$samplename'` instead of double quotes, like `"@RG\tID:$samplename"`, otherwise it will not work. ...
written 7 months ago by jrleary160
0
votes
1
answer
297
views
1
answers
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 7 months ago by jrleary160
0
votes
1
answer
297
views
1
answers
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 7 months ago by jrleary160

Latest awards to jrleary

Popular Question 6 months ago, created a question with more than 1,000 views. For Should I Run Clustering on PCA or t-SNE Components?
Supporter 10 months ago, voted at least 25 times.
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2216 users visited in the last hour