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Old 11-01-2012, 08:37 AM   #4
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Location: US

Join Date: Jan 2009
Posts: 392

Thats what I thought.

Even at 65 bp you may still have overlap and/or adaptor sequence.

Is it critical that you have paired end data? I had a similar situation with some paired end data. I simply dispensed with the second set of reads and treated it as single end reads. With that amount of overlap, its probably going to be impossible for tophat to get the insert size right.

Also try adaptor trimming with a trimmer that can handle variable lengths of adaptor sequence, I have used cutadapt with great success. Then try realigning without your paired end and you should have better results.

Otherwise....make a new library.
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