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Old 04-27-2016, 08:08 AM   #9
Jane M
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Location: Paris

Join Date: Aug 2011
Posts: 239

Originally Posted by GenoMax View Post
Default is 20 locations for multi-mapped reads for TopHat as I recall.

Originally Posted by GenoMax View Post
Those may be the optical duplicates that were generated by pad-hopping (or PCR during prep). You can try to run the Picard MarkDuplicates protocol (including the optical dup marking) and see if they get flagged. I have tried doing this with a limited number of samples from HiSeq 4000 but have not managed to get useful results for the optical part.

You can use the sequence of the human rDNA repeat found here to map against.
Thank you for these suggestions. I will try both, counting the number of reads flagged as optical duplicates and map the unmapped reads to ribosomal DNA, each time in the 2 experiments.

Originally Posted by GenoMax View Post
Perhaps you should allow multi-mappers to map at all locations. See if that ups the percentage. An academic exercise
Maybe I will try this after!
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