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NBISweden / workshop-RNAseq

Workshop • Analysis of RNA-seq data
https://NBISweden.github.io/workshop-RNAseq
GNU General Public License v3.0
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Creating Bed12 file - Use of NBIS tool? #3

Closed Juke34 closed 3 years ago

Juke34 commented 3 years ago

In the RseQC step you run 

 gtfToGenePred \
   references/annotations/Mus_musculus.GRCm38.101.gtf \
   references/annotations/Mus_musculus.GRCm38.101.genePred

 genePredToBed \
   references/annotations/Mus_musculus.GRCm38.101.genePred\
   references/annotations/Mus_musculus.GRCm38.101.bed

while it can be done in one step using AGAT developed by NBIS (available in conda and docker): agat_convert_sp_gff2bed.pl --gff Mus_musculus.GRCm38.101.gtf -o Mus_musculus.GRCm38.101.bed

If the result works as good it should be prefered, isn't it?

See here for more info: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_bed.md

royfrancis commented 3 years ago

I don't think there is a lot of benefit in adding a whole new dependency just for this one step.

Juke34 commented 3 years ago

For sure the benefit is really limited ^^