SAM flags for bowtie-Tophat

[dnusol]

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.

[nicolallias]

Sam flags have the same meaning whatever software produced it.
But I can be wrong :s

If I'm right, you're looking something like http://picard.sourceforge.net/explain-flags.html

On another hand, use samtools view -X for more (human-) readability than the hex flag.

[dnusol]

Thanks nicolallias, that is an interesting webpage.
So if I am not wrong, a Flag of 137 would mean that the read is part of a pair, that this read is aligned to the reference but its pair is unmapped, and this read is generated in the second round so comes from the s_N_2.sequence.txt file (in the case of illumina paired-end).

Is my interpretation correct?

[nicolallias]

I think so.

[frozenlyse]

Hi, given that TopHat and Bowtie align across splice junctions

Tophat does align across splice junctions, bowtie doesnt

Tophat does add some custom flags to reads eg the XS flag which describes which strand the RNA transcript likely originated from (deduced from splicing signals I believe)

[dnusol]

Thanks frozenlyse and nicolallias for your help.
Tophat seems to set some of the Bowtie arguments directly. I have not found in the manual what happens if one of the reads from a pair is not mapped to the reference. Is the mapped read used for transcript identification and the unmapped discarded or does Tophat discard both reads from the analysis?