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bgr files: change chromosome annotation

How would I change chromosome names with sed or awk from 1-22, X, Y to chr(1-22,X,Y)? Is there an expression that I can use?

sed bedgraph expressions awk
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updated by ATpoint ATpoint • written by TheCatalyst • TheCatalyst

Only see for changing the other away around, i.e. chr(1-22,X,Y) to 1-22, X, Y

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written by TheCatalyst • TheCatalyst

Basically awk '{print "chr"$X}' with X being the column where the chromosomes are in. Try to modify this minimal command to fit your needs, there are plenty of posts on that already that will inspire you to complete it.

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written by ATpoint ATpoint

Hi,

Could you post an example of your bgr file, please?

You can do this in terminal by typing:

head your_bgr_file.bgr

Make sure you highlight your example and click the 010101 button to code the example, so it's easier to copy and paste. You could also Edit your post and add it there.

-Pratik

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written by Pratik Pratik

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