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
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!
> 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
> > Best,
> > Tracy
> Jennifer Jackson
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at 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:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: