Question

Making API request to UCSC Genome API for T2T CHM13v2.0/hs1 DNA sequence

1

Entering edit mode

17 months ago

Yukthi ▴ 10

Has anyone had any luck making calls to the UCSC genome API for DNA sequences from the T2T CHM13v2.0 (hs1) assembly? I can easily make calls for hg38 (e.g. api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chr1;start=4321;end=5678), however making a call to the hs1 genome doesn't seem to be working. I've checked the list of available UCSC genomes (found here https://api.genome.ucsc.edu/list/ucscGenomes) and hs1 seems to be a valid genome to query, however I am only met with "Bad Request" status messages whenever I try to use it.

I'm sure that I'm just missing something small but some help would be greatly appreciated.

Thanks in advance!

UCSC T2T hs1 Genome • 943 views

ADD COMMENT • link 17 months ago by Yukthi ▴ 10

score 4 · Accepted Answer · 2022-12-23

I couldn't access hs1 too but there is another hub for T2T CHM13v2.0

Listing chromosomes

❯ curl 'api.genome.ucsc.edu/list/chromosomes?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt;genome=GCA_009914755.4'

Response:

{ "downloadTime": "2022:12:23T22:40:38Z", "downloadTimeStamp": 1671835238, "hubUrl": "https:\/\/hgdownload.soe.ucsc.edu\/hubs\/GCA\/009\/914\/755\/GCA_009914755.4\/hub.txt", "genome": "GCA_009914755.4", "chromCount": 25, "chromosomes": { "CP068254.1": 16569, "CP068257.2": 45090682, "CP068256.2": 51324926, "CP068259.2": 61707364, "CP086569.2": 62460029, "CP068258.2": 66210255, "CP068260.2": 80542538, "CP068261.2": 84276897, "CP068262.2": 96330374, "CP068263.2": 99753195, "CP068264.2": 101161492, "CP068265.2": 113566686, "CP068266.2": 133324548, "CP068268.2": 134758134, "CP068267.2": 135127769, "CP068270.2": 146259331, "CP068269.2": 150617247, "CP068255.2": 154259566, "CP068271.2": 160567428, "CP068272.2": 172126628, "CP068273.2": 182045439, "CP068274.2": 193574945, "CP068275.2": 201105948, "CP068276.2": 242696752, "CP068277.2": 248387328} } %

get sequence:

❯ curl 'api.genome.ucsc.edu/getData/sequence?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt;genome=GCA_009914755.4;chrom=CP068254.1;start=5;end=10'

Response:

{ "downloadTime": "2022:12:23T22:41:22Z", "downloadTimeStamp": 1671835282, "hubUrl": "https:\/\/hgdownload.soe.ucsc.edu\/hubs\/GCA\/009\/914\/755\/GCA_009914755.4\/hub.txt", "genome": "GCA_009914755.4", "chrom": "CP068254.1", "start": 5, "end": 10, "dna": "TGTAG"} %