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Forum: Bioinformatics 08-14-2013, 07:26 AM
Replies: 2
Views: 2,569
Posted By airad22
Yes I ran FastQC. The Per base sequence quality...

Yes I ran FastQC. The Per base sequence quality is in the green zone for all of them. In some the right reads are slightly lower than the left, but not much.

The only other thing I notice with ...
Forum: Bioinformatics 08-14-2013, 07:13 AM
Replies: 2
Views: 2,569
Posted By airad22
Unhappy Tophat RNASeq mapping - right reads map and left reads map 50% less

Hi!
I am trying to map RNA Seq (chick) with Tophat2 and I am getting low overall mapping rates (~30%). In the align_summary.txt file generated by Tophat2 - it appears that my right reads are mapping...
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