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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