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ZCGAOlab / ChTY001

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Issue about Chromosome Name in Gff3 file #1

Open fish2022Jul opened 7 months ago

fish2022Jul commented 7 months ago

Hi, Thank you for your work on T2T.YAO genome. But I found the chromosome name (chr1, chr2) in your gff3 file (YAO.hp.v1.1.gff3) don't fit that (GWHDQZI00000001, GWHDQZI00000002) in GWHDQZI00000000.genome.fasta. Is there any way to make them identical?

fish2022Jul commented 7 months ago

By the way, Is there any way I can got the vcf/bcf file for all the variants in YAO genome?

ZCGAOlab commented 7 months ago

By the way, Is there any way I can got the vcf/bcf file for all the variants in YAO genome? Besides, is the Vcf/bcf file for all the variants in YAO genome referring to variants compared to hg38 or chm13, or to our original read?

ZCGAOlab commented 7 months ago

Hi, Thank you for your work on T2T.YAO genome. But I found the chromosome name (chr1, chr2) in your gff3 file (YAO.hp.v1.1.gff3) don't fit that (GWHDQZI00000001, GWHDQZI00000002) in GWHDQZI00000000.genome.fasta. Is there any way to make them identical?

We are very sorry for the inconvenience caused to you. After querying the data, we found that GWHDQZI 000000 1 and GWHDQZI 000000 2 numbers were automatically generated by the GWH database. GWHDQZI 000000 1-GWHDQZI 000000 23 corresponds to the sequences of chr1-22 and the mitochondria. I think it can be replaced by some shell commands.

fish2022Jul commented 7 months ago

By the way, Is there any way I can got the vcf/bcf file for all the variants in YAO genome? Besides, is the Vcf/bcf file for all the variants in YAO genome referring to variants compared to hg38 or chm13, or to our original read?

I mean variants for YAO compared to hg38 (best) or chm13 (good)

fish2022Jul commented 7 months ago

Hi, Thank you for your work on T2T.YAO genome. But I found the chromosome name (chr1, chr2) in your gff3 file (YAO.hp.v1.1.gff3) don't fit that (GWHDQZI00000001, GWHDQZI00000002) in GWHDQZI00000000.genome.fasta. Is there any way to make them identical?

We are very sorry for the inconvenience caused to you. After querying the data, we found that GWHDQZI 000000 1 and GWHDQZI 000000 2 numbers were automatically generated by the GWH database. GWHDQZI 000000 1-GWHDQZI 000000 23 corresponds to the sequences of chr1-22 and the mitochondria. I think it can be replaced by some shell commands.

ok, got it