How Do I create a BED file from an hard masked fasta?

Question

[marcofraca]

Hi to everyone,

I would like to create a BED file with the position hard masked in a fasta file.

This is the hard masked fasta:

>seq1 
ACGTNNNNAGTCAGNNNNACGTC
>seq2
NNNNACGCATGNNNACGT

And this is the output bed file that I want:

seq1 5 9
seq1 16 19
seq2 1 4
seq2 12 14

[microfuge]

the twoBitInfo command from kentUtils (available here http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) has an option -nBed to get a bed file of N stretches. You will need to convert the fasta to twobit by another command twoBitToFa also available at the same site.

Answer 1

[Pierre Lindenbaum]

duplicate : Identifying long stretches of Ns ; Annotating/Finding "NNNNNN" scaffold gaps in genome assembly

[marcofraca]

Many thanks for these links. Your solution with flex work well.

[ATpoint]

Answer 2

[hewm2008]

This tools : https://github.com/BGI-shenzhen/Reseqtools by this : iTools Fatools findN -InPut in.fa -OutPut N_Region.bed