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 [Description: Description: Description: logo1a4Signature] 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<skype:nathanhaigh?call> Email: [email protected]<mailto:[email protected]> 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<https://twitter.com/watsonhaigh> @BIG_SA1<https://twitter.com/BIG_SA1> RID: B-9833-2008<http://www.researcherid.com/rid/B-9833-2008> ResearchGate: Nathan_Watson-Haigh<https://www.researchgate.net/profile/Nathan_Watson-Haigh/> ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
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