Reverse strand and first or second strand

[XG]

Dear Professors,

I have a question about the library type option in the command, if the RNA-seq data I used is reverse strand and I used pre-aligned bam file as input, which library type I should choose in the command line, fr-firststrand or fr-secondstrand ?

Thank you very much!

Best，
Xiao

[Xiao Lei]

It depends on the method of your library preparation, for example in my case, the library was prepared by the dUTP method, I use: --libType fr-firststrand in rMATS and it works well. 

Best,

Xiao

[kutsc...@gmail.com]

See this post for some additional details: https://groups.google.com/g/rmats-user-group/c/EDbNZV1Y-aU/m/-T1I1puzAAAJ

Eric