Hello Karen,
It sounds as if the data contains replicates, but this should be
confirmed with the data source by reviewing the methods for the specific
experiment.
If indeed these are replicates, it is best to process these
independently and submit them as replicates when using the NGS: RNA-seq
tools. The tool authors have specific advice regarding replicates at
their web site:
http://cufflinks.cbcb.umd.edu/howitworks.html#reps
If just different conditions, you would also want to process
independently - this is probably obvious but I wanted to mention it just
to be complete.
Links to resources, including a Galaxy tutorial, can be found grouped in
our wiki at:
http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server
Hopefully this helps,
Jen
Galaxy team
On 12/11/12 11:03 AM, Karen Margrethe Jessen wrote:
Hi,
I have downloaded the fastq.tgz files for an ENCODE RNA-SEQ data and
unpacked the files. The data set is paired end illumina. I am a bit
confused, as there are 5 files for read1 and 5 files for read2 for
each sample. Am I supposed to merge the 5 files before aligning to the
hg19 genome?
If yes, how should I merge these files?
I would greatly appreciate any help you can provide.
Best regards,
Karen Margrethe Jessen
Cand. Scient., ph.d.-student
Aarhus University
Denmark
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