Im having issues with my RNAseq libraries.
The library was made with the NexteraXT library which produces unstranded libraries. When I run tophat it only has one option "unstranded" so I set that. But after when it comes to cufflinks and/or cuffdiff there is an fr and and ff unstranded option. Does anyone know which ones I should chose based on their experiance or should I just leave both as "autodetect"?
Thanks Best wishes