Hello,

I am trying to do RNAseq analysis on Paired end data Illumina. I have about
4 files for each sample (2 forward and 2 reverse).

I want to analyze the data  in Galaxy.

Do I have to groom and run the QC for each file? Should I join the paired
files and run both tools on each pair, or should I combine all of the data
for each sample (which I don't know how to do) and then groom and run the
QC for all of the reads for the sample.

Ultimately, How do I run TopHat for paired-end data. When I select paired
end data in Galaxy, it gives an option to upload both files should I upload
both forward files once and reverse files once. Or should I combine both
the files before running the TopHat.

I am all confused. Any kind of help will be appreciated

Thanks in advance
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to