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
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
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