My first assumption was that the unmapped.bam output from Tophat 2 was ALL of the unmapped reads.
Since I am mapping different cultivar groups which possess a lot of variation, I tried both default settings and increasing the number of allowed mismatches. Increasing the number of allowed mismatches doubles the number of reads mapped, however, the reads in the unmapped.bam file are identical in number in both instances.
This doesn't add up.
I haven't found any reference to the unmapped.bam in the Tophat 2 manual, so if these are not ALL the unmapped reads, then what is it?
Since I am mapping different cultivar groups which possess a lot of variation, I tried both default settings and increasing the number of allowed mismatches. Increasing the number of allowed mismatches doubles the number of reads mapped, however, the reads in the unmapped.bam file are identical in number in both instances.
This doesn't add up.
I haven't found any reference to the unmapped.bam in the Tophat 2 manual, so if these are not ALL the unmapped reads, then what is it?