SAMtools and Tophat

[RockChalkJayhawk]

I mapped RNA-Seq using tophat. Then

samtools view -bS accepted_hits.sam > Hits.bam

But I get the following error:

The tag [ID] required for [PG] not present.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

Solutions?

[Thomas Doktor]

You need to provide samtools with a list of chromosome sizes using the -t option.

samtools view -bt chrom.sizes accepted_hits.sam > hits.bam

You don't need to include the -S option in this case.

See also the samtools manual: http://samtools.sourceforge.net/samtools.shtml