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Old 07-18-2016, 11:06 AM   #3
KamilSJaron
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Location: Switzerland

Join Date: Apr 2016
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Quote:
Originally Posted by dpryan View Post
Bit 2 denotes aligning as a "proper pair according to the aligner". Firstly, the alignments point away from each other. Secondly a 3kb fragment size is about 6-10x wider than expected. Are these mate-pair alignments? If so, you'll need to tell the aligner that.
Cheers Ryan!

Yes, these are mate-pairs (That is why I expected this insert size). Is it really important for mapper to know that the library is mate-pair library? It is already post-processed - therefore only difference to pair-end library is the insert size...

I have not realized before, that they do not point to each other. If this is the reason, what is the interpretation of this observation? Because there are about half of pairs without flag 2 (I have to check if all of them are pointing away from each other)
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