Tophat RNASeq mapping - right reads map and left reads map 50% less

[airad22]

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 at over 90% whereas the left reads are mapping at 30%. This is happening to all but one sample.
Has anyone ever encountered this or know how to resolve this?

This is the command I used:

tophat -p 8 -G gene_model.gtf -o Sample1 genome4 Sample1_1.fastq.gz Sample1_2.fastq.gz > Sample1.log 2>&1 &

Thanks in advance

Adi

[dpryan]

Did you run fastQC (or any other QC software) on these reads?

[airad22]

Did you run fastQC (or any other QC software) on these reads?

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 FastQC is that 'Sequence Duplication Levels' are very high (>=55.7%) . I don't know whether this could influence mapping though.

Thanks.