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.

Good luck with your project,

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!!


Yona Kim

Jennifer Hillman-Jackson
Galaxy Support and Training

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