Genes_on_Chr

Extract detailed information from Genes_on_Chr.R

Description

Genes_on_Chr.R can be used to draw the location of genes on chromosomes map quickly in PDF format based on the input data. It will become a useful tool for drawing genes on chromosomes map with the advantages of a simple input data format, easily modified output and very good portability. Genes_on_Chr.R is open source, so all we ask is that you cite our most recent paper in any publications that use this script:

基因基于R语言在染色体位置作图.
A tool to draw genes on chromosome based on R language.

Dependencies

All R versions

Getting started

Put Genes_on_Chr.R and data files in a same dir, then run:

Rscript  Genes_on_Chr.R  chr.txt  gene.txt

The structure of chr.txt (tab-delimited) data is: the first column is the chromosome number, and the second column is t信息学he base_pair of chromosome (Length):

1    Length_1
2    Length_2
3    Length_3
...  ...

The structure of gene.txt (tab-delimited) data is: the first column is the chromosome number, the second column is location of the gene, and the third column is name of the gene:

1    site_1       Gene_name_1
1    site_2       Gene_name_2
2    site_3       Gene_name_3
...   ...          ...

If you do not have the data files

1. Get chr.txt form genome.fa:
   

perl -e '$/ = ">"; while (<>) {($head, $seq) = split (/\n/, $_, 2); $len = length $seq; $head =~ /(\d+)/; print "$1\t$len\n";}' genome.fa > chr.txt

2. Get gene.txt form genome.gff:
   

perl  Search.pl  list.txt  GFF3.gff  >  gene.txt

Contact information

For any questions please contact [email protected]