getting exon coordinates
1
0
Entering edit mode
6 months ago
Xbox_27 • 0

How to get the exon co-ordinates of a particular gene?

genomics • 435 views
ADD COMMENT
0
Entering edit mode

Please do not use bioinformatics as a tag unless your post in about the field of bioinformatics itself.

ADD REPLY
1
Entering edit mode
6 months ago
ben@f ▴ 20

A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest and a text file with GeneName by line you can do something like :

grep -w -F -f geneofinterest.tsv yourannotationfile.gff | awk '{print $1,$2,$3, $4, $5}'|head

You can save and redirect the output to file

grep -w -F -f geneofinterest.tsv yourannotationfile.gff | awk '{print $1,$2,$3, $4, $5}' > genecoodinate.tsv

I hope this works for you

ADD COMMENT

Login before adding your answer.

Traffic: 2625 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6