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workshop-rnaseq's Issues

Creating Bed12 file - Use of NBIS tool?

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

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