Missing rMATS arguments

[adomingues]

Description of the bug

Not a bug as such, but more of a missing argument which is critical for rMATS.

one of the key rMATS arguments is libType (https://github.com/Xinglab/rmats-turbo?tab=readme-ov-file#all-arguments):

  --libType {fr-unstranded,fr-firststrand,fr-secondstrand}
                        Library type. Use fr-firststrand or fr-secondstrand
                        for strand-specific data. Only relevant to the prep
                        step, not the post step. Default: fr-unstranded

however in the rnasplice docs I don't see it exposed in the pipeline. Is is possible to choose the library type and I just missed?

Command used and terminal output

No response

Relevant files

No response

System information

No response

[jma1991]

Hello @adomingues

The library type parameter is inferred based on the value of the strandedness column in the input sample sheet file. See here.

If this solves your query, I will go-ahead and close the issue.

[adomingues]

Thanks @jma1991, that answers my question perfectly.