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Old 04-21-2016, 12:40 AM   #1
dhatziioanou
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Location: Greece

Join Date: Aug 2012
Posts: 8
Default counting Ns and gaps in scaffolds

Hello,

I have been trying to assemble some genomes and need a way to keep track of the number of gaps and NNs in my scaffolds. I've found ways to count everything else but not those.

I've been using abacas and gapfiller and in the beginning I was noting the number of gaps those programs mentioned until I found that they sometimes drastically disagreed on how many gaps I had.

Does anyone have a one liner command to count these or a little script I could use?

Thanks!
Diane
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