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Old 08-14-2013, 07:13 AM   #1
airad22
Junior Member
 
Location: Europe

Join Date: Aug 2013
Posts: 2
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 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
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