Why Tophat with either firststrand or secondstrand options produces the same XS?

Question

[biolab]

Dear all

I am curious of one of my recent results: when running TOPHAT2, I tried opposite --library-type options (fr-firststrand and fr-secondstrand). After samtools view bam_file | head command, I saw both results are the same. I suppose the XS should be opposite, but why they are the same? Hope to get your comments or answers. Thank you gratefully!

[Thibault D.]

Hi !

I have noticed somethig a bit different while trying to understand the TopHat's XS-Strand Attribute in BAM files : some of the XS-Strand attributes changes while the others keep the same value ... I don't understant this behaviour either (i.e. : 99 and 83 change, but 147 doesn't).

Have you notice that a single XS leads to both + or - (with a large predominance of one class) ?

Thanks.

[biolab]

Hi Thibault D, thanks for your comments. I am new using tophat and manipulating BAM file. I still need to learn more on FLAGs and XS meanings. Hope biostars experts provide some clues to our question.