qgen

A tool to annotate the coordinate. It is developed to easily get all gene informaiton from one coordinate.

Usage: ./qgen -f reference_file -i coordinates

• -f: the ucsc table formatted reference files (separated by ,)
• -i: the coordinates information (chr:coordinate:strand); the strand can be '*' if you are not sure about it. Multiple coordinates can be seperated by , or in a list file

example:

1. ./qgen -r example/20200508_NCBIRef_hg19_test.txt -i chr1:22021559:-
2. ./qgen -r example/20200508_NCBIRef_hg19_test.txt -i example/test.txt

Output:

• Gene : GeneName
• Chromsome: Chromsome
• Strand: Strand from gene
• Coordinate: Coordinate
• InputStrand: Strand from the input
• Transcripts: all transcripts
• UTR5: if the coordinate is in the UTR5 (following the transcripts orders, separated by ,)
• UTR3: if the coordinate is in the UTR3 (following the transcripts orders, separated by ,)
• Block: the block that the coordinate locates at, intron, exon, or intergenic (following the transcripts orders, separated by ,)
• BlockIndex: the block index that the coordinate locates at (following the transcripts orders, separated by ,)
• Frame: the frame infomation of the block that the coordinate locates at (following the transcripts orders, separated by ,)
• DisToStart: the distance to the block start of the coordinate (following the transcripts orders, separated by ,)
• DisToEnd: the distance to the block end of the coordinate (following the transcripts orders, separated by ,)

todo list:

1. compatible to the gtf format
2. infer the frame from two coordinates
3. Extract the mRNA or DNA sequece around a coordiante