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paulklemm/DEXSeq-RNACentral-Bug.sh

Created November 14, 2016 13:17
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DEXSeq prepare annotation throws error for RNACentral GTF file
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DEXSeq-RNACentral-Bug.sh
# Convert GFF3 to GTF file
wget ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/5.0/genome_coordinates/Mus_musculus.GRCm38.gff3.gz
gunzip --verbose Mus_musculus.GRCm38.gff3.gz
# Download gffread source and compile it
mkdir gffread_build
cd gffread_build
git clone https://github.com/gpertea/gclib
git clone https://github.com/gpertea/gffread
cd gffread
make
# 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 dexseq_count.py from the bioconductor GIT mirror
wget https://raw.githubusercontent.com/Bioconductor-mirror/DEXSeq/master/inst/python_scripts/dexseq_prepare_annotation.py
python dexseq_prepare_annotation.py Mus_musculus.GRCm38.gtf dexseq_prepare_annotation.out
# Yields the following error:
# Traceback (most recent call last):
# File "dexseq_prepare_annotation.py", line 54, in <module>
# f.attr['gene_id'] = f.attr['gene_id'].replace( ":", "_" )
# KeyError: 'gene_id'
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