Oakento / GTFanno

GTFanno

This script is for generating TSS, exon, intron, intergenic region annotations from GTF file. The input GTF file requires chromosome name with "chr" prefix.

Usage:

bash gtfanno.sh -f <GTF file> # Output file to current working directory

bash gtfanno.sh -f <GTF file> -o <output directory> -k # Includes scaffolds

Parameters:

• -f Required. Path to GTF file. Either gzipped or plain file is accepted.
• -p Optional. Prefix to output files. Default the same as the prefix of GTF file name.
• -o Optional. Output directory. Default the current working directory.
• -k Optional. Also include scaffolds.
• -r Optional. The radius upstream and downstream the TSS. Default to 300.
• -s Optional. The local chromosome size file for calculating intergenic area. If left empty, it will be automatically downloaded from https://github.com/igvteam/igv/tree/master/genomes/sizes
• -h Print this help message.