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Old 11-27-2013, 11:07 AM   #1
arcolombo698
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Default Quality Control on Local Machine/Server

Hello.

I have done all the merging of the fastq files on the server, so all the files are on the server.

However, my fastQC is installed locally. Is there a way to do QC on the server? or must I transfer all the files back locally to do QC?

Thank you
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Old 11-28-2013, 09:15 AM   #2
GenoMax
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FastQC will run fine on a unix server (long as java is available). You would need a X11 client on your local machine to project the GUI back to your desktop unless you have console access on the server.
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Old 12-02-2013, 11:31 PM   #3
colindaven
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On a server, try something like:
java -Xmx4g -jar Fastqc.jar *.fastq &

Fastqc will analyse all fastq files in the directory and save the results.
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Old 12-03-2013, 03:19 AM   #4
GenoMax
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If you are not interested in running in interactive mode (GUI) then you can indeed use the command line as Colindaven pointed out.

More information available here: http://www.bioinformatics.babraham.a...qc/INSTALL.txt Look for the section on "Running FastQC as part of a pipeline".
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