problem with RNA2MAP

[rlegendre]

Hi all,


I use RNA2MAp pipeline to predict new 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 ?



Thank you all,
Rachel

PS: sorry for my bad english !!

[KevinLam]

Hmmm is this a double post? I think the forum doesn't allow that