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ag1805x/GFF2GCcontent

Created August 22, 2019 10:35
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Code to extract GC% of genes from GFF file using bedtools
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GFF2GCcontent
###########################################
# Code to extract GC% of genes from GFF file
# using bedtools
# - Arindam Ghosh (22 August 2019)
###########################################
bedtools nuc -fi Homo_sapiens.GRCh38.dna.primary_assembly.fa -bed Homo_sapiens.GRCh38.84.gff3 | grep ID=gene:ENSG > temp.txt
echo -e "GeneID\tpct_GC" > GRCh38_GeneGC.txt
paste <(cut -d: -f2 temp.txt | cut -d';' -f1) <(cut -f11 temp.txt) >> GRCh38_GeneGC.txt
rm temp.txt
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