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ag1805x/gtf_2_geneLength

Created June 22, 2022 12:57
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gtf_2_geneLength
# Extract gene lengths from GTF file
# Download GTF file from https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files
echo "Gene_ID, Gene_name, Gene_type, Chr, Start, End, Gene_length" > gdc_gencode_v36_annotation.csv
awk '{if($3 == "gene") print $0}' gencode.v36.annotation.gtf | awk -F '[\t ;]' '{print $10","$16","$13","$1","$4","$5","$5-$4}' >> gdc_gencode_v36_annotation.csv
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