User: ekofman

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ekofman0
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Posts by ekofman

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Comment: C: bcl2fastq is interpreting my experiment folder structure incorrectly as MiSeq-st
... The directory tree looks exactly like the diagram for the NextSeq inputs in the Illumina documentation, and the run info xml looks like this (sorry the formatting is funky, assume all starting tags have appropriate corresponding closing tags): <\RunInfo xmlns:xsd="http://www.w3.org/2001/XMLSchem ...
written 3 months ago by ekofman0
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Comment: C: bcl2fastq is interpreting my experiment folder structure incorrectly as MiSeq-st
... bcl2fastq -r 8 -w 8 -p 8 --runfolder-dir 180320_NB501337_0390_AHLWLCBGX5 --output-dir 180320_NB501337_0390_AHLWLCBGX5/Data/Intensities/BaseCalls/ --sample-sheet sample.csv -r -w and -p are threading parameters ...
written 3 months ago by ekofman0
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bcl2fastq is interpreting my experiment folder structure incorrectly as MiSeq-style instead of NextSeq-style
... Hello, I am running bcl2fastq and getting the following error: Unable to find BCL file for 's_1_11101' in: 180320_NB501337_0390_AHLWLCBGX5/Data/Intensities/BaseCalls/L001/C1.1 It is very apparent based on the structure of my experiment directory (and my own outside knowledge, of course) that m ...
nextseq illumina fastq bcl2fastq bcl written 3 months ago by ekofman0 • updated 3 months ago by h.mon19k
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Mutect1 for WGS appropriate normal_panels attribute
... Hi, I'm running mutect1 with WGS and am trying to figure out what the appropriate attribute to use for the normal_panel is. I'm guessing it might be this 1000 genomes file ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analy ...
normals wgs panel mutect written 3 months ago by ekofman0

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