How To Get Gap Positions From Genome Fasta File

Question

[creepycomputing]

Hi,

First post here. Looks like you guys can really be helpful. I'm new to bioanalysis.

I have been looking on google extensively for an answer to the following question; without success so here I am.

I have a eukaryotic genome in fasta format. The file contains multiple scaffolds with assembly gaps (stretches of Ns). I would like to collect the "begin" and "end" positions of these gaps for all scaffolds.

Thanks in advance for your help..

[creepycomputing]

I apologize, I have finally found exactly the script I need here: https://www.uppnex.uu.se/userscripts/results/taxonomy%3A86

Cheers

[Lee Katz]

It's good karma to put your answer here even if you found it yourself