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Created November 14, 2016 13:17
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DEXSeq prepare annotation throws error for RNACentral GTF file
# Convert GFF3 to GTF file
gunzip --verbose Mus_musculus.GRCm38.gff3.gz
# Download gffread source and compile it
mkdir gffread_build
cd gffread_build
git clone
git clone
cd gffread
# convert GFF3 to GTF
gffread ../../Mus_musculus.GRCm38.gff3 -T -o ../../Mus_musculus.GRCm38.gtf
# Remove gffread_build again
cd ../../
rm -r -f gffread_build/
# Download from the bioconductor GIT mirror
python Mus_musculus.GRCm38.gtf dexseq_prepare_annotation.out
# Yields the following error:
# Traceback (most recent call last):
# File "", line 54, in <module>
# f.attr['gene_id'] = f.attr['gene_id'].replace( ":", "_" )
# KeyError: 'gene_id'
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