User: eric.londin

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eric.londin20
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2 years, 2 months ago
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e**********@jefferson.edu

Posts by eric.londin

<prev • 4 results • page 1 of 1 • next >
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bedtools coverage and paired-end data
... I have a question using bedtools with paired-end stranded RNA-seq data. Since one read is on the forward direction, and the second read is in the reverse direction, how does bedtools coverage handle these paired-reads when running it with the "-s" flag. For example, I am interested in getting covera ...
bedtools paired-end rna-seq written 3 months ago by eric.londin20
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combining overlapping vcf's into one
... Hi all, I have a question as to how to combine two separate VCFs into one large one. For example, say I have a dbSNP VCF and a Cosmic database VCF. I now want to merge or combine them into one file into a way that will produce a single file that contains the contents of both files. If there is an ov ...
vcf mergining vcfs written 9 months ago by eric.londin20
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Comment: C: Help with adding read groups in BWA bash loop script
... Sorry meant i instead of 1. Typo on my part - edited the original post ...
written 2.2 years ago by eric.londin20
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Help with adding read groups in BWA bash loop script
... Hi all, I'm relatively new to bash scripting and working on one to map samples with BWA bash-loop. My loop is the following: for i in $(ls *.fastq.gz | rev | cut -c 10- | rev | uniq) do ./bwa mem -t 60 -c 1 -R '@RG\tID:${i}\tSM:${i}\tPL:illumina\tPU:Lane1\tLB:exome' MyReference.fq $ ...
next-gen bwa bash-loop written 2.2 years ago by eric.londin20 • updated 2.2 years ago by WouterDeCoster42k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Help with adding read groups in BWA bash loop script

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