Regarding combining several txt files and producing one fastq file

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Regarding combining several txt files and producing one fastq file

Jen Hillman-Jackson
Hi Yona,

To merge together multiple datasets this way, use the tool "Text
Manipulation -> Concatenate datasets tail-to-head". This works on two
datasets at a time, so you may need to run it a few times if you have
more than that, adding in a new file to the master merged file with each
run.

Watch out for introducing blank lines (unintentionally) between the
files. To remove them should any be present (it doesn't harm a file if
none are there), after you have merged all the files together, use the
tool "Filter and Sort -> Select" with:
    option: NOT Matching
    and the expression: ^$

Once you are sure that the merged file is correct, you can permanently
delete the working files to recover disk space. "FastQC" and/or "FASTQ
Groomer" are generally both good at detecting format problems.
http://wiki.galaxyproject.org/Support#Error_from_tools

Good luck with your project,

Jen
Galaxy team

On 4/27/13 8:23 PM, Yona Kim wrote:

> Dear Jennifer
>
> I was wondering if there is a tool in galaxy that combines several txt
> files (which I got from decompressing fastq.tgz file) and produce one
> fastq file from them.
>
> I was searching it in google and read your previous email to somebody
> else and you mentioned about the tool "cat" which seems to be the
> right tool for me to use to combine these txt files in order to
> produce one fastq file.. but I can't find this tool..
>
> any advice?
>
> Thank you very much and I always appreciate your help very much!!
>
> Bests,
>
> Yona Kim
>
>

--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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Jennifer Hillman-Jackson
http://galaxyproject.org