Question

Human Genome

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2.9 years ago

akshitiz09 ▴ 10

Hi,

Does any one know where I can find GRCH37 build with chr1 instead of Accession Number (NC_000001.10)? Or if there is an easy way to for conversion.

Thank you

GRCH37 • 707 views

ADD COMMENT • link updated 2.9 years ago by a.alnawfal.1992 ▴ 240 • written 2.9 years ago by akshitiz09 ▴ 10

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Have you googled this? There are tools out there that can reheader FASTA files, and NCBI has pages mapping NC_ accession numbers to chromosome names. For GRCh37.p13, that page is: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25

You can download the full sequence report to perform the mapping locally.

ADD REPLY • link 2.9 years ago by Ram 43k

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Hi Ram, Yes I have googled it and somehow things are not working. I haven't checked the NCBI pages but I will look into now and see if it works.

Thank you

ADD REPLY • link 2.9 years ago by akshitiz09 ▴ 10

score 0 · Answer 1 · 2021-06-12

Hi akshitiz09, I notice that the Reference in NCBI "Recently" changed to the notation that you mentioned! There is a way for conversion, but I believe downloading each chromosome from UCSC then join them together is a better solution "Which is use".

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/

download Major chromosome "Chr1-22 + X, Y, and MT" only, then use cat command on Linux/Mac OS terminal to concatenate all chromosomes in the same order. "Ex: cat Chr1.fa.gz Chr2.fa.gz .... ChrMT.fa.gz > Homo_sapiens_Hg19.fa.gz".

Now you have your reference genome and you can use it.

Wish you all the best! Abdullah