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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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FEELnc_filter.pl kicks out all monoexonic transcript although --monoex was set to -1 #24

Closed JJBio closed 6 years ago

JJBio commented 6 years ago

Hi @tderrien,

I have a set of novel transcripts from stringtie. I prefiltered the candidates with gffcompare and only used class codes i, u and x and fed those into the FEELnc pipeline. I have strand-specific data hence I set --monoex=-1 but it still kicks out ALL monoexonic RNA candidates. So my command was FEELnc_filter.pl -i prefilteredCandidateTrans.gtf -a gencode.v27.annotation_proteinCoding.gtf --monoex=-1 -p 20 I also tried the line below but I wasn't sure about the usage of -b - I am using gencode annotation, which uses transcript_type instead of transcript_biotype FEELnc_filter.pl -i prefilteredCandidateTrans.gtf -a gencode.v27.annotation.gtf -b transcript_type=protein_coding --monoex=-1 -p 20 I using v0.1.0.

Thanks for your help!

tderrien commented 6 years ago

Hi @JJBio ,

Indeed, the FEELnc_filter.pl should not kick out the single-exon transcripts that are transcribed in antisense to mRNAs exons (if you used the --monoex=-1 option). It's hard to tell what's going on without the example/input file prefilteredCandidateTrans.gtf. Do you want to send (part of) it so that I can have a look? All the best!