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Filter number of N's fasta file

Heys,

Once again I need your programming help. I have a lot of fasta files made out of 1Mb sliding window along a reference genome. As there areas in the genome that are not really well sequenced or that the sample has not a lot of data, I would like to remove the files where at least one sample has half of the information as N. How could I do that?

Thanks a lot in advance!

bash programming fasta
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updated by GenoMax GenoMax • written by gubrins gubrins

where at least one sample has half of the information as N

i don't understand.

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written by Pierre Lindenbaum Pierre Lindenbaum

sorry Pierre. Each one of my fasta files has 1Mb of information. I would like to know if any sample within each fasta file has 50% or more bases as N.

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written by gubrins gubrins

Counting N'S Within Fasta

You can use stats.sh program from BBMap suite to generate the base distribution (only relevant part is posted here). You can easily see files where N content would be > 50%.

$ stats.sh in=t2.fa
A   C   G   T   N   IUPAC   Other   GC  GC_stdev
0.2394  0.2810  0.1935  0.2861  0.0096  0.0000  0.0000  0.4745  0.0000
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written by GenoMax GenoMax

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