getting exon coordinates
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4 weeks ago
Xbox_27 • 0

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

genomics • 314 views
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Please do not use bioinformatics as a tag unless your post in about the field of bioinformatics itself.

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4 weeks 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

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