Question

The annotation about human genome

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7.9 years ago

whaiyu06 ▴ 80

What is the difference between Homo_sapiens.GRCh38.84.chr.gtf.gz and Homo_sapiens.GRCh38.84.gtf.gz on the Ensembl genome browser?If the latter contain the former? What about Homo_sapiens.GRCh38.84.chr_patch_hapl_scaff.gtf.gz?

rna-seq ensembl • 1.7k views

ADD COMMENT • link updated 4.4 years ago by Biostar 20 • written 7.9 years ago by whaiyu06 ▴ 80

score 3 · Answer 1 · 2016-05-31

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7.9 years ago

Denise CS ★ 5.2k

I'm sorry to say that @WouterDeCoster's reply is not correct. The .gtf.gz file contains all sequences assembled into chromosomes as well as sequences not placed on chromosomes. The .chr.gtf will contain sequences assembled into chromosomes only. This is not clear from the README files, so the explanation will be included in there from release 85, due in July.

ADD COMMENT • link 7.9 years ago by Denise CS ★ 5.2k

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Thank you very much for your reply！

ADD REPLY • link 7.9 years ago by whaiyu06 ▴ 80

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Oops, will edit my answer to reflect that mistake and avoid confusion.

ADD REPLY • link 7.9 years ago by WouterDeCoster 47k

score 1 · Answer 2 · 2016-05-31

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7.9 years ago

WouterDeCoster 47k

!See answer of Denise below!

[ignore this]

Homo_sapiens.GRCh38.84.chr.gtf.gz contains chromosomes as integers ('1', '2', '22',...) and Homo_sapiens.GRCh38.84.gtf.gz uses 'chr'-notation ('chr1', 'chr2', 'chr22',...)

[/ignore this]

ADD COMMENT • link 7.9 years ago by WouterDeCoster 47k