[Bioperl-l] Trimming low quality reads

[shalabh sharma]

@chris,
     Thanks for the suggestions, as i have mentioned earlier that i have
very huge dataset, so before starting anything i am trying to run few test
to see the efficiency of seqTrim, so i can avoid converting fasta to fastq.

Thanks
Shalabh

On Wed, Feb 16, 2011 at 12:36 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Ah, you need qual filtering tied to a specific fasta file.  As most tools
> like fastx expect FASTQ input, it might be advisable to convert to FASTQ
> (which Bio::SeqIO::fastq does if I'm not mistaken).
>
> chris
>
> On Feb 16, 2011, at 11:28 AM, shalabh sharma wrote:
>
> > Hi ,
> >       Thanks all for valuable suggestions, actually i was looking at
> FASTX tool kit but at i glance i saw that the quality filter is only
> implemented for FASTQ files and not for fasta files.
> > But i will take a look again.
> >
> > Thanks
> > Shalabh
> >
> >
> > On Wed, Feb 16, 2011 at 12:10 PM, Ben Bimber <bbimber at gmail.com> wrote:
> > Fastx is great and we use those tools in a number of places, but If
> > I'm not mistaken, doesnt its trimming involve filters their either
> > including or excluding the read as a whole, rather than end clipping?
> >
> > The need probably depends on your data.  With short reads, I could
> > imagine that's what you want.  With 500bp 454 reads, end clipping is
> > nice.  I ended up making a simple little (and not terribly efficient)
> > script that does 3' end clipping.  My datasets are orders of magnitude
> > smaller than what you posted though....
> >
> > -Ben
> >
> >
> >
> >
> > On Wed, Feb 16, 2011 at 10:59 AM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > > +1 on using fastx.  I believe this is what our local seq pipeline uses
> prior to us sending out the processed stuff.
> > >
> > > chris
> > >
> > > On Feb 16, 2011, at 10:41 AM, Jason Stajich wrote:
> > >
> > >> I would use a faster implementation like the fastx toolkit -
> http://hannonlab.cshl.edu/fastx_toolkit/
> > >>
> > >> There are lots of answers to NGS questions on seqanswers too
> > >> http://www.google.com/search?q=site:seqanswers.com+trim
> > >>
> > >>
> > >> Jordi Durban wrote:
> > >>> Well, there's a program called Seqtrim that uses bioperl to trim the
> > >>> sequences.
> > >>> Here more information:
> > >>> http://www.scbi.uma.es/cgi-bin/seqtrim/seqtrim_login.cgi
> > >>> Hope this helps.
> > >>>
> > >>> 2011/2/16 shalabh sharma<shalabh.sharma7 at gmail.com>
> > >>>
> > >>>> Hi,
> > >>>>    Is there any bioperl module available to quality trim in
> fasta-qual
> > >>>>  format.
> > >>>> i am little worried about the efficiency as i have huge data (~ 50
> gb).
> > >>>> Also i would really appreciate if some one has some other
> suggestions.
> > >>>>
> > >>>> Thanks
> > >>>> Shalabh
> > >>>> _______________________________________________
> > >>>> Bioperl-l mailing list
> > >>>> Bioperl-l at lists.open-bio.org
> > >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >>>>
> > >>>
> > >>>
> > >>>
> > >>
> > >> --
> > >> Jason Stajich
> > >>
> > >>
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> > >
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>
>