Question: no accepted_hits.bam generated
gravatar for zhang.wen81
4.4 years ago by
United States
zhang.wen810 wrote:



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!

rna-seq • 1.1k views
ADD COMMENTlink modified 4.4 years ago by nalandaatmi70 • written 4.4 years ago by zhang.wen810

Did you check log files?

ADD REPLYlink written 4.4 years ago by cpad011212k
gravatar for nalandaatmi
4.4 years ago by
United States
nalandaatmi70 wrote:

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.

ADD COMMENTlink written 4.4 years ago by nalandaatmi70
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