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Old 12-07-2018, 04:47 AM   #4
sfh838t
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Location: Mountain Grove, MO, USA

Join Date: Apr 2014
Posts: 29
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Thank you GenoMax.
the header suggestion almost worked, in one case, not so much in the other because it is too long I suspect.
and thanks for the BBsplit suggestion as well.It obviously does alignment along the way, but does not mention anything about the aligner and since I work with very short reads, <30 nt, that can be an issue.
either way, what I really needed to see was the alignments, so I ended up using excel and making histograms from the SAM files.
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