getting exon coordinates

Question

[Xbox_27]

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

[Pierre Lindenbaum]

Get genomic coordinates from gene names ;
extracting the exons coordinates on hg38 ;
Intron and exon coordinates of all genes from Hg19 ;etc...

[Ram]

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

Answer 1

[ben@f]

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