Hi all! Thank you for making this pipeline! I’m reasonably new to transcript assembly (some toe dipping with Stringtie) and am keen to try out your creation! I’ve got a couple of questions: • I’m using Seqera Platform to launch the pipeline. I’m using Trinity as the assembler. The field shown below suggests that I only need to set the strand-specificity for rnaSPAdes but I thought this would need to be set for Trinity as well?

Hi Christel, Looks like the creators of Trinity do have a parameter for setting strand specificity. I haven't included this as a separate field in the pipeline, but I can do this in a future release. For now, you will need to enter it under the

extra_trinity_args

field. You can enter

--SS_lib_type RF

(or replace

RF

with

FR

or

F

or

R

). Trinity documentation about which option you should choose is here.

Thank you for your reply! Getting back onto this now!