problem with RNA2MAP

[rlegendre]

Hi all,


I use RNA2MAp pipeline to predict novels miRNA in horse genome using SOLID data. But, I dont understand how the filtering step work ? I know Mapread is use but how adapters are removed ? Only adapters in 3' are trimmed or all adapters ?

Moreover, the gff file is used for what ? What is the process ? all the reads are mapped in the reference genome and next knows miRNA
are identified and reads appears as unknows miRNA are save in a file ? Or only reads appears as knows miRNA are mapped in genome ?

I'd like use many reference files of miRBase with many organism, it's possible with RNA2Map ?



Thank you all,
Rachel

PS: sorry for my bad english !!

[KevinLam]

Sorry do not have the answers to your questions, but did you manage to get the RNA2MAP to work? I have problems at the generation of the bash scripts stage hence I gave up.

[rlegendre]

Yes, RNA2map is working perfectly with the sample data, but not with my SOLID data... The main problem was presence in the bin directory of RNA2Map of necessary scripts for Corona and when you start pipeline, Corona don't find these scripts. You must copy bin's script of RNA2map in bin's of Corona, and pipeline will work... normally !!

I hope to have help you !!!

[KevinLam]

Hmmm I do have bioscope installed along with RNA2MAP maybe that's what's causing the problems.
will create a new acct just for RNA2MAP I guess.
Thanks for the tip!