Dear forum,
I have RNASeq SOLID data that is paired end. I want to use Tophat to perform the alignment. Does anyone out there know how to
ensure that "even if an end of a pair could not be aligned, it should still have an entry"
Aaron Quinlan requested that I ensure that this is so -- because I went to use BEDtools with the -pe option and it failed saying my data was not sorted -- he suggested that it may be because I did not ensure that the pair every seq had an entry even if it was not aligned....
Best,
Anne
I have RNASeq SOLID data that is paired end. I want to use Tophat to perform the alignment. Does anyone out there know how to
ensure that "even if an end of a pair could not be aligned, it should still have an entry"
Aaron Quinlan requested that I ensure that this is so -- because I went to use BEDtools with the -pe option and it failed saying my data was not sorted -- he suggested that it may be because I did not ensure that the pair every seq had an entry even if it was not aligned....
Best,
Anne
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