Originally posted by BADE
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I would suggest you perform a 'HEADCROP' of 3 bp on the data, immediately after the ILLUMINACLIP step, and before the other quality filtering steps. This will simply drop the problem bases entirely from all reads.
Alternatively, you could widen the window/lower the threshold of the SLIDINGWINDOW, which would help bridge these dodgy patches. However, even after getting the dodgy data past the trimming stage, you still have the issue of aligning it so the HEADCROP might be better.
You might also want to consider more liberal alignment settings in Tophat, since many of the reads are probably failing due to these poor quality bases.
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