hg18 GTF

[Tuur Muyldermans]

Dear,

 

For reproducing an old paper we would like to use the GTF file accompanied of the hg18 reference genome. However, on the website where I downloaded the hg18 reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/hg18/bigZips/) I couldn’t find the annotation file. Is there any other location where I could find it?

 

Thanks in advance,

Best regards,

Tuur

 

Tuur Muyldermans – ELIXIR Bioinformatics Trainer

 

ELIXIR Belgium | VIB Bioinformatics Core

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[Matthew Speir]

Hello, Tuur.

Thank you for your question about GTF files for the human assembly hg18.

Can you provide us with the context in which the UCSC Genome Browser was mentioned in this paper? If you can give us the paragraph or paper itself, that would be great. We want to make sure that we are pointing you to the correct track and context of the paper. 

Thank you!

Matthew Speir

UCSC Genomics Institute

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[Tuur Muyldermans]

Dear Matthew,

 

Please find attached the pdf of the paper. In fact, the UCSC Genome Browser was not mentioned in the paper explicitly, nor the reference to the reference genome. However, from the data we have we saw the ‘chr1’ meaning that it is UCSC and not Ensembl for example.

If you do a CTRL/CMD+F in the paper and type ‘hg18’ you’ll get two hits. The second one will tell us that it was mapped on hg18 and basically that’s all… I can still e-mail the author and ask whether he has more information, but since I was just searching for a GTF file, I thought I should mail you …

 

Thanks a lot for your reply, really appreciate that you want to help!

 

Kind regards,

Tuur

[Matthew Speir]

Hello, Tuur.

Thank you for providing the PDF of the paper. That was helpful.

We don't provide pre-made GTF files for the hg18 assembly. At this time, we do provide some for more recent assemblies like hg38 but, when the paper was written, we did not provide them for any assemblies. It doesn't look like they used the UCSC Genome Browser in the paper, rather they used IGV for visualization.

If you want to replicate what the authors did, I would reach out to them and see what GTF or gene file they used for their analysis.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genomics Institute