After performing the alignment with bbmap.sh, the resulting SAM file contains both the sequence identifier and the description of each sequence from the FASTA file in the RNAME (reference sequence name) field. htseq-count does not seem to be able to handle these and annotates all reads as '__no_feature'.
Am I missing something here?
Other than "brute force", is there a tool to fix the SAM files?
Again, thanks for any pointers and feedback!
Am I missing something here?
Other than "brute force", is there a tool to fix the SAM files?
Again, thanks for any pointers and feedback!
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