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:
Nathan_Watson-Haigh
______________________________________________________________________
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
______________________________________________________________________