How to download Refseq annotation gtf file

[Aritra Deb]

Hello,

I'm looking for the RefSeq genome reference .gtf files (both GRCh37 and GRCh38) for bulk RNAseq data analysis. Is it available from UCSC genome browser database? Previously I downloaded and used the file 'GCF_000001405.40_GRCh38.p14_genomic_fixed.gtf' from NCBI. But it gave an error [Error: no valid ID found for GFF record] while running StringTie. Please let me know where and how to download the correct file. Thanks.

Aritra Deb

Research Fellow

The Wellcome-Wolfson Institute for Experimental Medicine

School of Medicine, Dentistry and Biomedical Sciences

Queen's University Belfast

97 Lisburn Road
Belfast
BT9 7BL

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can find the NCBI RefSeq GTF files for hg38 and hg19 on the hgdownload server.

hg38:

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz

hg19:

https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/genes/hg19.ncbiRefSeq.gtf.gz

I hope this is helpful. 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.

Jairo Navarro
UCSC Genome Browser

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[Hong-Seok Ha]

Hello,

I would like to inquire about obtaining RefSeq GTF or BED12 files for all versions in hg19. For example, for an entry like NM_xxxxxx.4, I need files that include all versions, such as NM_xxxxxx.1, NM_xxxxxx.2, NM_xxxxxx.3, and NM_xxxxxx.4. When I search RefSeq Genes data, I can see information on previous versions, but they are not available for download via the Table Browser. Could you please let me know if there is a way to obtain files that contain all versions of the RefSeq data?

Thank you very much.
Hongseok Ha

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

For questions about data access, most tracks have a "Data Access" section that should guide you through most of your questions. For example, the NCBI RefSeq track for hg19:

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr7&g=refSeqComposite

On that page, there is a link to the archives for this track:

https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg19/ncbiRefSeq/

I hope this is helpful. 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.

Jairo Navarro
UCSC Genome Browser

On Fri, Nov 1, 2024 at 3:30 AM Hong-Seok Ha <empero...@gmail.com> wrote:

Hello,

I would like to inquire about obtaining RefSeq GTF or BED12 files for all versions in hg19. For example, for an entry like NM_xxxxxx.4, I need files that include all versions, such as NM_xxxxxx.1, NM_xxxxxx.2, NM_xxxxxx.3, and NM_xxxxxx.4. When I search RefSeq Genes data, I can see information on previous versions, but they are not available for download via the Table Browser. Could you please let me know if there is a way to obtain files that contain all versions of the RefSeq data?

Thank you very much.

[Aritra Deb]

Hello,

Thank you very much! Your previous email helped me a lot for the differential analysis of RNA-seq data considering RefSeq Hg19 as reference (hg19.ncbiRefSeq.gtf). Now my question is if I want the gff3 file for this 'hg19.ncbiRefSeq.gtf' then where/how I can get it? If there is any repository from where I can download the gff3 file then please let me know. Alternatively, if there is any tool which can be used to create gff3 file from a gtf file please let me know how to use it. Thanks.

Dr. Aritra Deb

Research Fellow

Centre for Public Health

School of Medicine, Dentistry and Biomedical Sciences

Institute of Clinical Science B

Queen's University Belfast

Royal Victoria Hospital

97 Lisburn Road
Belfast
BT12 6BJ

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From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: 06 June 2024 00:18
To: Aritra Deb <A....@qub.ac.uk>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] How to download Refseq annotation gtf file

 

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[Matthew Speir]

Hello, Aritra.

Two of our engineers share that many pipelines they've encountered are compatible with both GTF and GFF3. This is because GTF is a functional subset of GFF3. Could you share why you need GFF3 specifically instead of GTF?

We only provide GTF files and we don't have any tools for converting files into GFF3. But there are several tools available online. One is Galaxy (https://usegalaxy.org/) which has an interface for gffread that can be used for converting other formats into GFF3.

I hope this is helpful. 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.

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Matthew Speir

UCSC Genome Browser, User Support

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/AS4PR07MB8827E5E754EF0139F5234C65AC3D2%40AS4PR07MB8827.eurprd07.prod.outlook.com.

[Aritra Deb]

Hello,

Apologies for a delayed reply. I somehow missed your email. The reason I'm looking for GFF3 along with GTF is that I'm trying to perform a differential splicing analysis for RNA-seq data. For this purpose I'm using the MAJIQ/VOILA method(https://biociphers.bitbucket.io/majiq-docs/index.html). I have used this method with Gencode Grch38 reference where both GTF and GFF3 is available, and that worked fine. Now I'm trying to run the same with Refseq hg19 reference, as this is required for further analysis. I tried to convert the GTF to GFF3 but it didn't work. So I'm looking for a correct GFF3 or a proper tool to convert from GTF to GFF3. Hope this has explained the situation. Thanks.

Aritra

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From: Matthew Speir <msp...@ucsc.edu>
Sent: 13 December 2024 23:03
To: Aritra Deb <A....@qub.ac.uk>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>; Jairo Navarro Gonzalez <jnav...@ucsc.edu>

Subject: Re: [genome] How to download Refseq annotation gtf file

 

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[Matthew Speir]

Hello, Aritra.

NCBI provides annotation files in both GTF and GFF format on their website: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/. If you need more details about the specific files, there is a README in that directory.

I hope this is helpful. 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.

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Matthew Speir

UCSC Genome Browser, User Support

[Maximilian Haeussler]

Hi Aritra,

> I tried to convert the GTF to GFF3 but it didn't work.

As Matt mentioned, the tool gffread should produce valid GFF3s from most files that vaguely look like GFF or GTF, it can fix up most common GFF problems and should produce valid GFF3 files: 

$ gffread input.gtf -o output.gff3

If its output is not accepted by your pipeline, you may contact the pipeline's author or the gffread author.

I've seen "gtf_to_gff3" mentioned on the internet from GenomeTools, but have never tried it.

best

Max

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