How long running FEELnc_codpot.pl step takes? (FEELnc long-non coding RNAs)

Question

[SHN]

Hello All,

I am running for long non-coding RNAs analysis using a FEELnc software (on human data). I found my candidate LncRNAs (first step) and now am running the second step using the coding potentials) using FEELnc_codpot.pl.

My code is as below: Is my code correct for this step? How long this step takes time, s I have been running it for 24 hours and it still is not finished.

FEELnc_codpot.pl -i ~/RNASeqData/FEELnc/Result/candidate_lncRNA.gtf -a ~/RNASeqData/FEELnc/Result/feelncCodingPot_1/genome.gtf -g ~/RNASeqData/FEELnc/feelncCodingPot_1/genome.fa -b transcript_biotype=protein_coding --mode=shuffle

Appreciate your comments and help, SN

Answer 1

[Thomas]

Hello,

Sorry for the delay in our reply!

You may want to try the -n,--numtx=undef Number of transcripts required for the training in the annotation [ default undef ]

This will select a subset of transcripts for training the model (e.g. 5000,5000) instead of the whole gtf file.

Cheers,