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# create hsapiends annotation for small rna analisis
FINAL="srna-transcripts.gtf"
if [ -e $FINAL ] ; then
rm $FINAL
fi
if [ ! -e hsa.gff3 ] ; then
wget ftp://mirbase.org/pub/mirbase/20/genomes/hsa.gff3
fi
awk '$3=="miRNA"' hsa.gff3 | sed 's/=/ /g' >> $FINAL
if [ ! -e wgRna.txt.gz ] ; then
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz
fi
zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> $FINAL
if [ ! -e tRNAs.txt.gz ] ; then
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/tRNAs.txt.gz
fi
zcat tRNAs.txt.gz | awk '{print $2"\t.\ttRNA\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> $FINAL
if [ ! -e rmsk.txt.gz ] ; then
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz
fi
zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> $FINAL
if [ ! -e refGene.txt.gz ] ; then
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
fi
zcat refGene.txt.gz | awk '{print $3"\t.\tgene\t"$5"\t"$6"\t.\t"$4"\t.\tname "$13";"}' >> $FINAL
if [ ! -e piR_hg19_v1.0.bed.gz ] ; then
wget http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
fi
zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> $FINAL
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