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Old 03-11-2011, 03:04 AM   #1
Junior Member
Location: washington area

Join Date: Mar 2011
Posts: 7
Default Tophat paired end alignment.

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....

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