no accepted_hits.bam generated

Question

[zhang.wen81]

Hi,

I am using tophat to do map alignment for RNA-seq. There is no accepted_hits.bam file that generated. While in the tmp folder, all the temporary files are kept and all bed files are ok. I tried several times and divided the original fastq.gz file into several pieces but still for each piece, the same problem exists. Could I combine all the accepted_hits files in the tmp directory to get the accepted_hits.bam file?

Thanks a lot!

[cpad0112]

Did you check log files?

Answer 1

[nalandaatmi]

Hi Zhang,

Try checking the log files (run.log and tophat.log). It will give a good notion either the program got terminated or completed successfully.

tail alignment/logs/run.log

You should be seeing samtools sort step of all accepted_hits.bam. Then samtools merge of all sorted accepted_hits.bam.