Hi,
given that TopHat and Bowtie align across splice junctions, are there any flags in the SAM-formatted output different to, say, BWA alignment flags? what would be the flag for unaligned paired-end reads?
Cheers,
D.
given that TopHat and Bowtie align across splice junctions, are there any flags in the SAM-formatted output different to, say, BWA alignment flags? what would be the flag for unaligned paired-end reads?
Cheers,
D.
Comment