Hi Jennifer,
just out of curiousity, is the command a linux cat? or does it actually
parse the fastq sequences?
asking as my service provider actually just split my PE files by lines (not
no. of reads ) in fastq

assuming that I can't merge them in galaxy, I am merging them properly then
splitting them again (anyway i can map using concurrent processes and merged
the bam later on

Cheers
Kevin

On Fri, Oct 28, 2011 at 10:30 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:

> Hi Tracy,
>
> The tool "Text Manipulation -> Concatenate datasets tail-to-head" can put
> the two together. Then set the datatype to fastq, if needed (click on the
> "pencil" icon for the full dataset to reach the "Edit Attributes" form to
> make the change).
>
> Be sure to watch out for an extra newline being added between the two
> files. You can test for/eliminate this using "Filter and Sort -> Select"
> with the options "that: NOT Matching" and "the pattern: ^$".
> (the regular expression '^$' [no quotes] matches empty lines).
>
> I am sending to the galaxy-user mailing list for our internal tracking and
> for other users to learn from. Please send all questions directly to the
> list going forward, it is very helpful for us.
>
> Thanks for using Galaxy!
>
> Jen
> Galaxy team
>
>
>
> On 10/27/11 11:58 AM, Qingquan Liu wrote:
> > Hi Jennifer,
> >
> > I have sequenced one sample on 2 lanes of GAII, and now I am trying to
> > merge the 2 fastq files. How should I do it on Galaxy? Thank you very
> much!
> >
> > Best,
> >
> > Tracy
> >
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/**Support<http://galaxyproject.org/wiki/Support>
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