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Old 03-08-2016, 09:11 AM   #1
carolW
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Default sam input of tmap

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
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Old 03-08-2016, 10:06 AM   #2
GenoMax
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Have you considered converting that sam to fastq and then using that as an input?
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Old 03-08-2016, 10:19 AM   #3
carolW
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True that could get around the problem.

Cheers,
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