How To Create Masked Genome?

Question

[Bioscientist]

Now I have build-18 genome at hand; also duplication/satellites bed files (coordinate). I want to mask those satellites/duplications by replacing their sequences into 'NNNNN'

How can I do this? (I download repeat sequences from UCSC genome broweser, can we also download such masked genome from somewhere?)

THanks

Answer 1

[Pierre Lindenbaum]

Bedtools contains a tool named: maskFastaFromBed

Masks a FASTA file based on BED coordinates.

BTW: the following directory contains a 'masked' version of hg18:http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/

chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case.

[Bioscientist]

works super!!!!

[Louis Kok]

maskFastaFromBed does not seem like working to mask only one base. I have tried to mask only one base but couldn't make it. For example, I would like to mask position 20 in Chr. The bed files are as below:

Chr    20     20         or          Chr    20     -

Both cases actually mask position 20 and 21.

Is there any option I can include to only mask one base?

[Louis Kok]

By the way, I have also tried maskseq from EMBOSS and it works well to mask only one base. However, I wish to mask aligned sequences but maskseq removes the gaps which I want to retain. maskFastaFromBed does not remove the gaps while performing masking.

[Louis Kok]

Just figured out that if you want to extract position 20, you need to prepare the bed file like: Chr 19 20.