[Bioperl-l] Trimming low quality reads

[Chris Fields]

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
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>