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Old 03-07-2017, 10:03 AM   #4
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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BBMap is going to give you an absolute answer by actually using the data that is there. There is no ambiguity involved. It will work if you have a reference available or without. Only case it won't work is if you have reads that don't merge and you don't have a reference available.

If you are able to join the PE reads then there are some inserts there that are smaller than 300 bp.

While you library may have had fragments in the 600 bp range, if there were any that were of a smaller size (as indicated by tails on bioanalyzer traces, you don't get an an absolute answer from bioanalyzer, AFAIK) then those fragments will preferentially bind and form clusters.

Last edited by GenoMax; 03-07-2017 at 10:10 AM.
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