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The annotation about human genome

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
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updated by Biostar 380 • | written by whaiyu06 8

2 answers

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.

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written by Denise CS 525

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

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written by WouterDeCoster 4.8K

Thank you very much for your reply！

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written by whaiyu06 8

!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]

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written by WouterDeCoster 4.8K

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