does accepted_hits or unmapped .bams from tophat2 include reads mapping to junctions?

[Kennels]

Hi

Does anyone know if the 'accepted_hits.bam' file from the tophat2 output include reads that were mapped to junctions? I did not use the 'fusion-search' option.
If so, what tags are used in the .bam file to identify these? I can't find relevant information in the tophat page.
Or are these included in the unmapped.bam file?

thanks

[kopi-o]

Yes, the accepted_hits.bam file includes them. Look for 'N' characters in the CIGAR string (6th column).