Tophat: --library-type option

[blanco]

When using the --library-type option in Tophat the corresponding .sam file produces "XS:A:+" or "XS:A:-" flags for almost all hits.

Am I right to infer that these flags tell you from which strand the read came from? So, all hits with the "XS:A:+" flag come from the plus strand and vice verse.

I am running a strand specific libraries from the dUTP method. So in Tophat I added the option: --library-type fr-firststrand.

Any input on this would be most appreciated, thanks.

blanco

[blanco]

After some research and correspondence with folks from the community I have confirmed that the XS:A tag indeed infers from which strand the read comes from.

Just in case some people are wondering the same.

blanco