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 much!
> Best,
> Tracy

Jennifer Jackson
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