can'nt choose "Types Supported library" between ff-en-unstranded and fr-unstranded

Question

[Bioiris]

Hi;

i have RNA-seq data (BAM files) and i know that is unstranded, but when I want to quantify with cuffdiff, I can'nt choose "Types Supported library" between ff-en-unstranded and fr-unstranded is there any method to know if my data are ff-en-unstranded or fr-unstranded ??

Thanks.

[Fabio Marroni]

Where did you find " ff-en-unstranded"? I couldn't find it in cuffdiff manual.

[Bioiris]

sorry it was an error, I wanted to say ff-unstranded

Supported library types: ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand fr-unstranded (default) transfrags

[Fabio Marroni]

In my version of cuffdiff (2.2.0) I see the same libraries you showed. Reading on the online manual, they list only fr-unstranded (default), fr-firststrand and fr-secondstrand, and they say "For paired-end data, we currently only support protocols where reads are point towards each other.". I don't know which info is correct. However, I guess it is more likely that you had a fr-unstranded library (i.e. the standard paired-end). Finally, if I am not wrong, it is possible that cufflinks is able to detect the platform and protocol (according to the manual; I have to admit that I always specified the protocol so I never paid attention to this detail).