sam input of tmap

[carolW]

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

[GenoMax]

Have you considered converting that sam to fastq and then using that as an input?

[carolW]

True that could get around the problem.

Cheers,