# This script is used for pre-process genome gtf files prepare the genome annotation file as input, for human the inputs are: gencode.v19.annotation.gtf,gencode.v19.tRNAs.gtf,miRbase_hsa.gff3,gencode.v19.long_noncoding_RNAs.gtf et al you can use the input in /data1/users1/chaodi/ncRNA/human/gff/Gencode19/Input for testing ! you will get these results: 1. separated specific biotypes 2. seperated 5' and 3' UTR 3. defined intergenic region 4. cleaned gtf for cufflinks the output files are in output: output_dir/separate_gff output_dir/merge_gff output_dir/clean_gtf/