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# create hsapiends annotation for small rna analisis
# cel235
FINAL="srna-transcripts.gtf"
if [ -e $FINAL ] ; then
rm $FINAL
fi
if [ ! -e cel.gff3 ] ; then
wget ftp://mirbase.org/pub/mirbase/21/genomes/cel.gff3
fi
awk '$3=="miRNA"' cel.gff3 | sed 's/=/ /g' >> $FINAL
if [ ! -e Caenorhabditis_elegans.WBcel235.81.gtf.gz ] ; then
wget ftp://ftp.ensembl.org/pub/release-81/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.81.gtf.gz
fi
zcat wgEncodeGencodeBasicVM4.txt.gz | grep -v exon >> $FINAL
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