I need to use featureCounts on the public available data from encode project for mm9 from Bing Ren lab. As far as I understood, the rna-seq is strand specific but I need to know the library type (ff-firststrand, ff-secondstrand, ff-unstranded, fr-firststrand, fr-secondstrand, fr-unstranded) to specify correctly the -s parameter of the featureCounts:
-s <int> Indicate if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default.