I am trying to do RNAseq analysis on Paired end data from the Hiseq2000.  I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files).

I think that I need to:

-convert them into FASTQ sanger format using the FASTSQ groomer tool

-check the quality using the FASTQqc tool

I don't know how to handle this many files.  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.

Thanks in advance for advice

Lindsey