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From: | Nathan S. Watson-Haigh |
Subject: | Parallelising grep |
Date: | Fri, 9 Aug 2013 05:53:46 +0000 |
I have a SAM/BAM file and I’d like to grep for alignments of certain reads IDs. I have the read ID strings in another file. I’m currently doing this with: $ samtools view in.bam | fgrep -w -f read.ids > alignments.txt Is it possible to parallelise the grep by having each grep process a different subset of read iDs from the read.ids file? Or is there an alternative way to parallelise this which I have overlooked? Cheers, Nathan -- Nathan S. Watson-Haigh, PhD Research Fellow in Bioinformatics Australian Centre for Plant Functional Genomics (ACPFG) School of Agriculture, Food and Wine University of Adelaide Waite Campus Plant Genomics Centre Hartley Grove, Urrbrae SA 5064 Phone: +61
8 8313 2046 Mobile: +61 438 711 615 Skype:
nathanhaigh Email:
nathan.haigh@acpfg.com.au Web:
http://www.acpfg.com.au/bioinformatics LinkedIn
http://www.linkedin.com/profile/view?id=114191748 Github:
https://github.com/nathanhaigh/
https://gist.github.com/nathanhaigh/ Twitter:
@watsonhaigh RID:
B-9833-2008 ResearchGate:
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