User: eric.londin

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eric.londin30
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Posts by eric.londin

<prev • 7 results • page 1 of 1 • next >
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Comment: C: cram file to fastq conversion
... That was the problem. just had to sort the cram file, and worked fine. Thanks for the help ...
written 9 weeks ago by eric.londin30
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Comment: C: cram file to fastq conversion
... Thank you. I got that reference and still getting an error. samtools fastq --reference GRCh38.fa -1 out.R1.fastq -2 out.R2.fastq input.cram > Failed to populate reference for id 0 Unable to fetch reference #0 9999..134549 Failure to decode slice [M::bam2fq_mainloop] processed 0 reads So, I ...
written 9 weeks ago by eric.londin30
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cram file to fastq conversion
... Hi all, I received some cram files from the 1000 genomes data. I am trying to convert them back to a fastq file, but can't seem to figure out how to do this. I've tried using samtools fastq -1 out.R1.fastq -2 out.R2.fastq input.cram but when doing this, I get an error of: > Failed to popul ...
fastq cram conversion written 9 weeks ago by eric.londin30 • updated 9 weeks ago by lieven.sterck8.6k
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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 14 months ago by eric.londin30
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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 19 months ago by eric.londin30
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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 3.1 years ago by eric.londin30
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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 3.1 years ago by eric.londin30 • updated 3.1 years ago by WouterDeCoster44k

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Popular Question 3.1 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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