Question: How to identify the haplotypes in the Venter diploid genome
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gravatar for olga.botvinnik
4.2 years ago by
United States
olga.botvinnik80 wrote:

Has anyone managed to download Venter's diploid genome? I've downloaded the fasta file from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/ - have to click each chromosome individually and then click "HuRef" in that folder) but it's unclear which scaffolds are haplotypes of what. Here's some example headers from chromosome 10. 

>gi|157812129|ref|NW_001837930.2| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279188237, whole genome shotgun sequence
>gi|157812130|ref|NW_001837931.2| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279188232, whole genome shotgun sequence
>gi|157812131|ref|NW_001837932.2| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279188217:11934018-19557365, whole genome shotgun sequence
>gi|157696810|ref|NW_001837933.1| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279187939, whole genome shotgun sequence
>gi|157696811|ref|NW_001837934.1| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279185051, whole genome shotgun sequence
>gi|157696812|ref|NW_001837935.1| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279181895, whole genome shotgun sequence
>gi|157812132|ref|NW_001837936.2| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279180355, whole genome shotgun sequence
>gi|157812133|ref|NW_001837937.2| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279181459, whole genome shotgun sequence
>gi|157812134|ref|NW_001837938.2| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279182485, whole genome shotgun sequence
>gi|157696816|ref|NW_001837939.1| Homo sapiens chromosome 10 genomic scaffold, alternate assembly HuRef SCAF_1103279188024, whole genome shotgun sequence

Do you know which are the haplotypes?

 
venter diploid fasta genome • 1.2k views
ADD COMMENTlink modified 4.2 years ago by Istvan Albert ♦♦ 77k • written 4.2 years ago by olga.botvinnik80
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