one of the input format that tmap accepts is sam. I have generated sam file from basecaller bam with samtools view -h which contains lines starting with @PG and @RG and the raw reads. When I map with tmap, all the reads are unaligned.
Is there any problem with the sam formatting? When I don't generate sam with headers, I get the err msg from tmap @RG is out of bound. So that's why I generated with -h.
Look forward to your reply,
Carol
Is there any problem with the sam formatting? When I don't generate sam with headers, I get the err msg from tmap @RG is out of bound. So that's why I generated with -h.
Look forward to your reply,
Carol
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