SAMtools reports error when converting Tophat's result

[Jack Lee]

Dear SEQanswers fellows, I had a problem of outputting result of Tophat. I've searched this forum and googled to find a answer but nothing I can use to solve this problem.

I got an error message when Tophat almost finished an analysis of 100M tags of a SOLiD 50SE RNA-seq.

The error message was:
Parse error at line 23113384: sequence and quality are inconsistent

I tried to convert the accepted_hits.sam to BAM by SAMtool command but the error showed again.

My software environment is:
Ubuntu 10.10
Bowtie 0.12.7
Tophat 1.1.4
SAMtools 1.11

Could someone give me a clue of what's happened?

Thank you very much.


Jack