[Bioc-sig-seq] QA for Bowtie

[Martin Morgan]

"Eyad Almasri" <ealmas1 at uic.edu> writes:

> Hello
>
> I want to ask if when qa() will be available for bowtie alignment files?

Hi Eyad --

It's available now (ShortRead 1.2.0, available with the current
release of Bioconductor)

  qa <- qa(dirPath, pattern, type="Bowtie")
  browseURL(report(qa))

for a bit of speed try

  library(Rmpi)
  mpi.spawn.Rslaves(nsl=as.many.as.bowtie.files.or.nodes.in.cluster)

before qa (the input and some processing steps can be quite time /
memory intensive).

Martin

> Thanks
>
> Eyad
>
>
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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