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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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FEELnc_filter.pl -b transcript_biotype=protein_coding #54

Closed TluckDucky closed 1 year ago

TluckDucky commented 2 years ago

Hello there,

I'm running the FEELnc_filter module in two approaches, as follows:

-i taco-new-assembly.gtf -a gencode.v40.primary_assembly.annotation.gtf -b transcript_biotype=protein_coding --monoex=0 -p 16 -o FEELnc_filter-1stStranded.log > 1st-strandedTFBfiltered.gtf &

and

-i taco-new-assembly.gtf -a gencode.v40.primary_assembly.annotation.gtf --monoex=0 -p 16 -o FEELnc_filter-1stStranded.log > 1st-strandedTFBfiltered.gtf &

When I checked the results, I got the same number of transcripts (35.395) , and I was expecting to get a larger number using the second approach since I haven't provided the option -b transcript_biotype=protein_coding, why is that? I read some stuff here and on internet, studied my data but couldn't figure it out.

May you help me, please?

Thanks in advance

vwucher commented 2 years ago

Hi,

Sorry for the delay of the answer. GENCODE change their name for the biotype. It is now called type. Did you try running the command with -b transcript_type=protein_coding?

Hope this help! Valentin