[Bioperl-l] reverse complement of fastq

shalabh sharma shalabh.sharma7 at gmail.com
Thu Aug 30 16:01:10 EDT 2012


Hey Chris,
              Thanks a lot it worked and it was really fast.

Thanks
Shalabh

On Thu, Aug 30, 2012 at 2:54 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> If you want something that gives you revcom *very quickly*, Bioperl is
> sadly not the way to go just yet.  However, you can use something like
> seqtk, which is very fast:
>
>     https://github.com/lh3/seqtk
>
> Something like this should work:
>
> $ seqtk seq -r orig.fq > rc.fq
>
> chris
>
> On Aug 30, 2012, at 1:07 PM, shalabh sharma <shalabh.sharma7 at gmail.com>
> wrote:
>
> > HI,
> >     I have a fastq file with few million reads. I need to find reverse
> > complement of the reads.
> > I used 'revcom' method but its not working for fastq.
> >
> > I will really appreciate if anyone can help me out.
> >
> > Thanks
> > Shalabh
> >
> >
> > --
> > Shalabh Sharma
> > Scientific Computing Professional Associate (Bioinformatics Specialist)
> > Department of Marine Sciences
> > University of Georgia
> > Athens, GA 30602-3636
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


More information about the Bioperl-l mailing list