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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