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
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