Do reads from the illumina mate-pair need to be reverse-complemented prior to alignment?
On a somewhat unrelated note, I have noted that the insert size estimation from bfast is not anywhere near what I would expect. I am not using ungapped pairing nor am I providing a std dev for insert size. Is this expected? If not, do you have a guess as to why this may be the case? When I run the same data in bwa (or assemble with velvet), the estimated insert size if right-on, so I don't think it's a library issue.
On a somewhat unrelated note, I have noted that the insert size estimation from bfast is not anywhere near what I would expect. I am not using ungapped pairing nor am I providing a std dev for insert size. Is this expected? If not, do you have a guess as to why this may be the case? When I run the same data in bwa (or assemble with velvet), the estimated insert size if right-on, so I don't think it's a library issue.
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