Hi Tony,

Yes, that should work too. I have written up a BioPerl hack that indexes the
reads and pulls out the pairs that is chugging away right now. If that does
not work out somehow, I will give your idea a shot. Thanks!

Best,
Surya

On Tue, Mar 29, 2011 at 4:20 PM, Barbet,Anthony F <bar...@ufl.edu> wrote:

> Can you not do fastq join on the 2 files, fastq filter for the single (same
> max and min bases) full length combined size (and quality if you want), then
> fastq splitter?
>
> Tony
> ________________________________________
> From: galaxy-user-boun...@lists.bx.psu.edu [
> galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Surya Saha [
> ss2...@cornell.edu]
> Sent: Tuesday, March 29, 2011 4:00 PM
> To: Anton Nekrutenko
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Combining the paired reads from Illumina run
>
> Hi Anton,
>
> Thank you for the tip. The sequence names do end in /1 and /2 but that can
> be fixed using Manipulate FASTQ tool, right?
>
> -Surya
>
> On Tue, Mar 29, 2011 at 3:46 PM, Anton Nekrutenko <an...@bx.psu.edu
> <mailto:an...@bx.psu.edu>> wrote:
> >
> > You can try converting fastq to tabular (NGS: QC and Manipulation).
> Jointing (Join, Subtract and Group) the two files on ids (provided they do
> not have /1 and /2). Splitting into two files with cut (Text manipulation),
> and going back into fastq with tabulat-to-fastq (NGS: QC and Manipulation).
> With 30 mil reads this will likely take some time though.
> > Thanks,
> > anton
> >
> > On Mar 29, 2011, at 11:38 AM, Surya Saha wrote:
> >
> > These are Illumina reads
> >
> > -S.
> >
> > On Tue, Mar 29, 2011 at 11:37 AM, Anton Nekrutenko <an...@bx.psu.edu
> <mailto:an...@bx.psu.edu>> wrote:
> >>
> >> Are these illumina or solid reads?
> >>
> >> Tx,
> >>
> >> anton
> >>
> >>
> >> On Mar 29, 2011, at 11:29 AM, Surya Saha wrote:
> >>
> >> > Hi,
> >> >
> >> > I have two fastq files with the forward(/1) and reverse(/2) paired
> reads. The reads are not in same order in either file, some pairs are
> absent/missing and the files are 8 GB each with abt 30 mill reads each.
> >> >
> >> > I am trying to pull out all the paired reads for which both fwd and
> rev exist. Can I use a combination of fastq tools in Galaxy to do this?
> >> >
> >> > Thanks!
> >> >
> >> > -Surya ___________________________________________________________
> >> > The Galaxy User list should be used for the discussion of
> >> > Galaxy analysis and other features on the public server
> >> > at usegalaxy.org<http://usegalaxy.org>.  Please keep all replies on
> the list by
> >> > using "reply all" in your mail client.  For discussion of
> >> > local Galaxy instances and the Galaxy source code, please
> >> > use the Galaxy Development list:
> >> >
> >> >  http://lists.bx.psu.edu/listinfo/galaxy-dev
> >> >
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> >> > please use the interface at:
> >> >
> >> >  http://lists.bx.psu.edu/
> >>
> >> Anton Nekrutenko
> >> http://nekrut.bx.psu.edu
> >> http://usegalaxy.org
> >>
> >>
> >>
> >
> >
> > Anton Nekrutenko
> > http://nekrut.bx.psu.edu
> > http://usegalaxy.org
> >
> >
>
>
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