Quality Control on Local Machine/Server

[arcolombo698]

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

[GenoMax]

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.

[colindaven]

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.

[GenoMax]

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".