Hello! I am new to RNA-seq, but I have to conduct a transcriptome analysis and DEs of lncRNA.
Currently, I’m at the stage of discovering nоvel lncRNAs and facing some difficulties.
The tool GFFcompare generates several output files, but two of them are important to me - annotated transcripts and TMAP. I would like to filter GFFcompare output, so to get only transcripts with class_code “u, i, x” and exons>=2.
The TMAP file contains all the necessary attributes; I can filter by columns using “Filter data on any column using simple expressions” or Select lines that match an expression" or , but the file is tabular, and I need a GTF result. On the other hand, I can’t filter annotated transcripts file because It doesn’t contain all the attributes there.
My questions are:
How should I proceed, which GFFcompare output to choose, and which Galaxy filter tools should I use?
Is it possible that if I decide to filter the TMAP, I can then convert the tabular file to GTF?
I will be grateful for any guidance and advice you can provide!