Filter number of N's fasta file

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3.0 years ago

gubrins ▴ 350

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 • 794 views

ADD COMMENT • link updated 3.0 years ago by GenoMax 148k • written 3.0 years ago by gubrins ▴ 350

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

i don't understand.

ADD REPLY • link 3.0 years ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link 3.0 years ago by gubrins ▴ 350

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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

ADD REPLY • link 3.0 years ago by GenoMax 148k

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