How to extract intervals for regions that are masked?

Question

[serpalma.v]

Hello

I want to determine the begining and end of each interval formed only by Ns (masked region). Then I would like to split the chromosome into smaller intervals to keep the regions that are not masked.

For example:

AGGTCGTTNNNNAACTGNNAGTC

I would like to get three intervals from this sequence: AGGTCGTT -> from 1 to 8 AACTG -> from 13 to 17 AGTC -> from 20 to 23

Is there a tool I could use to do the task? I have been searching, but I cannot find the right one.

Thanks!

[Pierre Lindenbaum]

duplicate: Split sequence according the 'N' base

[serpalma.v]

It does not give the intervals of the regions that are not masked. That is what I really need.

[wm]

The "Genome" subtract the "masked" intervals are the "unmasked" intervals, this is what you want, right?

You can get it using bedtools complement command:

First, you need generate the Genome file for your genome

$ cat in.fa   
>fa   
AGGTCGTTNNNNAACTGNNAGTC   

$ samtools faidx in.fa    
$ cat in.fa.fai   
fa      23      4       23      24

Second, get the location of masked intervals, (answered by "shenwei356" link from previous post, see above link)

$ seqkit locate  -P -p '[Nn]+' in.fa --bed > masked.bed    
$ cat masked.bed    
fa      8       12      [Nn]+   0       +    
fa      17      19      [Nn]+   0       +

Last. get the unmasked intervals

$ bedtools complement -i in.bed -g in.fa.fai    
fa      0       8    
fa      12      17    
fa      19      23