Non-repeat human genome dataset

Question

[Ivan]

Could anyone please point me to where I could find a dataset of non-repeat sequences for the human ref genome. I'm not sure if it's still regarded as true, but I saw that possibly 2/3 of the human genome contains repeats. Is there a place where I can download the other 1/3 of the human genome without repeats. Non-repeats of any human ref genome version would be good, but the best ones would be hg19 or hg38.

Answer 1

[jseg]

Hello,

I believe you're looking for genome sequences of the human genome, without repeats. Such sequences are termed masked sequences.

If you use Bioconductor, you can use the BSgenome.Hsapiens.UCSC.hg38.masked package.

If you want a FASTA file directly, you can download the masked sequences here: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.masked.gz

There are more info on the file at this link: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips

I hope this helps !

Best wishes.