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Old 11-01-2012, 08:18 AM   #3
Location: Ireland

Join Date: Oct 2012
Posts: 42

I've trimmed the reads using fastq_quality_trimmer & filter and fastx_trimmer.

One of the problems I've had is that the RNA fragment size is ~130 bp (post adapter removal) and my 100bp reads therefore overlap considerably. I've been using fastx_trimmer to cut the reads to 65bp to ensure no overlap - but they don't seem to be pairing properly in mapping.

I haven't checked for adapters - I ran the .txt files through fastqc and there were no over-represented sequences.

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