This script is for generating TSS, exon, intron, intergenic region annotations from GTF file. The input GTF file requires chromosome name with "chr" prefix.
bash gtfanno.sh -f <GTF file>
# Output file to current working directory
bash gtfanno.sh -f <GTF file> -o <output directory> -k
# Includes scaffolds
-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.