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 <jen@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
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