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!