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Old 02-25-2015, 05:25 AM   #5
JMFA
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Location: Portugal

Join Date: Nov 2010
Posts: 11
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This is actually 100bp PE DNAseq data.
I've clipped the adapter sequences and the Kmer profile looks much better (not perfect but better)!

However, I have an additional question.
While running cutadapt to remove the adapter sequences I am also setting the "-m" option (used to throw away processed reads shorter than N bases) to 100bp. However, I end up discarding approx. half of the reads this way.

Is there a problem (for instance, in the alignment step) to use reads with varying length?
Again, thank you very much for the input.
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