User: MMa

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MMa220
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Posts by MMa

<prev • 29 results • page 1 of 3 • next >
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Answer: A: ssGSEA on RNA-Seq data from TCGA
... I know this is an old thread, but SSGSEA can be calculated using the Bioconductor package GSVA. If you use RPKM, use `ssgsea <- gsva (RPKM, method="ssgsea", kcdf="Gaussian", ...)`; if you use raw counts, use `ssgsea <- gsva (counts, method="ssgsea", kcdf="Poisson", ...)` ...
written 3 days ago by MMa220
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Comment: C: How to get sequencing depths from VCF with Rsamtools
... The docs for the current versions of pindel states depth is the same I'd get from `samtools depth`. ...
written 4 months ago by MMa220
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How to get sequencing depths from VCF with Rsamtools
... I got from our collaborator some pindel output and the BAM files that is used as pindel input. Unfortunately, they used an older of version of pindel (before approximately 0.2.4u) that doesn't record total depth at breakpoint (i.e. the DP field in VCF). While our collaborator's standard practice is ...
R rsamtools pindel written 4 months ago by MMa220 • updated 3 months ago by Pierre Lindenbaum100k
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Comment: C: bcftools: how to annotate a file with a larger file using bcftools annotate?
... If you did that successfully on a different file yesterday, then check whether the smallfile.vcf you're using today have been indexed. ...
written 4 months ago by MMa220
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Comment: C: bcftools: how to annotate a file with a larger file using bcftools annotate?
... I mean the `bcftools annotate` command line. ...
written 4 months ago by MMa220
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Comment: C: bcftools: how to annotate a file with a larger file using bcftools annotate?
... What exactly was the command line you used? bcftools output gzipped vcf by default, so try renaming OCT1.genome_min.vcf to OCT1.genome_min.vcf.gz and retry. ...
written 4 months ago by MMa220
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Answer: A: bcftools: how to annotate a file with a larger file using bcftools annotate?
... It's actually more of `bcftools annotate -a largefile.vcf -c [comma separated of INFO tags you want to transfer in the form of DST_TAG:=SRC_TAG] smallfile.vcf` ...
written 4 months ago by MMa220
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Search VCF by ID in Python
... I've been trying to find a python driver for VCF that allows me to search the VCF by one or more IDs without me writing loops, but I haven't found any that doesn't use databases. Does parsers like that exist, or do I really need to use a database for that? ...
python snp written 4 months ago by MMa220
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Comment: C: Converting MuTect v1 text outputs to VCF
... library (vcfR) MT12VCF <- function (inputFile, outFile){ inputDF <- read.delim (inputFile, stringsAsFactors=F) if ((length(unique(inputDF$normal_name)) > 1) || (length(unique(inputDF$tumor_name)) > 1)){ stop ("This function assumes ...
written 5 months ago by MMa220
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Answer: A: Converting MuTect v1 text outputs to VCF
... Since the comment above implied there isn't, eventually I wrote one in R that should provide all the fields that `-vcf` emits; but since the raw MuTect text out doesn't give out the raw DP, the DP is derived as the sum of the two ADs. This script is also based on the assumption that MuTect1 only em ...
written 5 months ago by MMa220

Latest awards to MMa

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Different results with edgeR when adding gene symbols
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Different results with edgeR when adding gene symbols
Scholar 6 months ago, created an answer that has been accepted. For C: I get the same modules but different number of genes WGCNA
Scholar 6 months ago, created an answer that has been accepted. For C: I get the same modules but different number of genes WGCNA

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