User: Jeremy Leipzig

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Posts by Jeremy Leipzig

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Job: RNA Computational Biologist at Panorama Medicine in Philadelphia
... Job description: Panorama Medicine is seeking an experienced RNA Computational Biologist with a strong RNA biology background to analyze large-scale RNA data at their Philadelphia office. Responsibilities: Analyze large-scale RNA-seq data. Discover underlying mechanisms of observed data results. ...
job rna-seq written 9 weeks ago by Jeremy Leipzig70
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Comment: C: is the Rsamtools::pileup example broken?
... same after update to Rsamtools_1.30.0 and RNAseqData.HNRNPC.bam.chr14_0.16.0  ...
written 11 months ago by Jeremy Leipzig70
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is the Rsamtools::pileup example broken?
... BiocInstaller::biocLite(("RNAseqData.HNRNPC.bam.chr14")) BiocInstaller::biocLite("Rsamtools") library(Rsamtools) library("RNAseqData.HNRNPC.bam.chr14") fl <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1] res <- pileup(fl) head(res) > res <- pileup(fl) > > head(res) [1] seqnames pos ...
rsamtools pileup written 11 months ago by Jeremy Leipzig70 • updated 11 months ago by Martin Morgan ♦♦ 22k
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VariantAnnotation as.vranges with asterisk in ALT field
... GATK has recently started using asterisks in the ALT field for certain variants (i believe a SNP and deletion at one site) chr22 47461908 . TAA * 859.92 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=-3.105;ClippingRankSum=0.773;DP=119;FS=12.256;MLEAC=2;MLEAF=0.333;MQ=70;MQRankSum=0.042 ...
variantannotation gatk written 2.8 years ago by Jeremy Leipzig70 • updated 2.8 years ago by Michael Lawrence10k
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Comment: C: need additional sanity checks in TabixFile or readVcf
... Valerie, Thanks. You will get the same cryptic error if you use the wrong file as the TabixFile. vcfFile <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") from <- vcfFile to <- tempfile() compressVcf <- bgzip(from, to) idx <- indexTabix(compressVcf, "vcf") rng <- G ...
written 5.3 years ago by Jeremy Leipzig70
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Comment: C: need additional sanity checks in TabixFile or readVcf
... well that's odd. managed to get the same error using the most kosher workflow I could find: > vcfFile <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") > from <- vcfFile > to <- tempfile() > compressVcf <- bgzip(from, to) > idx <- indexTabix(compressVcf, ...
written 5.3 years ago by Jeremy Leipzig70
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need additional sanity checks in TabixFile or readVcf
... I think the Bioconductor workflows for variant studies are great, but TabixFile or readVcf might need some additional sanity checks. If a careless user (not me of course - I'm asking for a friend) mistakenly assumes a VCF is the "TabixFile" and the vcf.bgz.idx is the Tabix index, they will get this ...
written 5.3 years ago by Jeremy Leipzig70 • updated 5.3 years ago by Martin Morgan ♦♦ 22k
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extending XString to facilitate miRNA editing
... Hello, I would like to apply the notion of "edits" on individual reads (as opposed to pileups or other aggregates) to examine post-transcriptional miRNA editing. I was thinking the best way to do this would be to inherit and extend XString virtual class with named integers. setClass('XStringWithEdi ...
mirna written 7.3 years ago by Jeremy Leipzig70 • updated 7.3 years ago by Michael Lawrence10k

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For need additional sanity checks in TabixFile or readVcf

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