Canfam4 UU GSD1.0 gene annotations

[Brian Williams]

Hi,

I am a postdoc at UMN and working on a canfam4 remapping project. While looking at the Genome Browser, I saw that there was a track that had UU GSD1.0 gene annotations. I was hoping to find someone to help me locate this annotation. I can't seem to find it on the website, but I could just be missing something. Would it be possible for someone to direct me to where these files are located?

Best,

Brian

[Luis Nassar]

Hello, Brian.

Thank you for your interest in the Genome Browser.

Those annotations for the canFam4 browser (http://genome.ucsc.edu/cgi-bin/hgTracks?db=canFam4) were supplied by the Lindblad-Toh group (https://lindbladtohlab.org/). The annotation files we display can be found on our download server at the following location:

http://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/uuGene.txt.gz

We also have the following two datasets from the same group:

SNP and indels track vcf: https://hgdownload.soe.ucsc.edu/gbdb/canFam4/bbi/altAllele/
Structural variations: http://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/structVar.txt.gz

If you have specific questions regarding the data, you can direct those towards the Lindblad-Toh lab (https://lindbladtohlab.org/contact/). They also provide a paper for citing the data (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=canFam4&c=chr14&g=uuGene).

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAM%3DX-LyX%3DqcFVPd6B%3DMGaPA7ZUX%2BRZGcooX9h4_706wt5bNtFw%40mail.gmail.com.

[Brian Williams]

Hi Luis,

Thanks for getting back to me. Is there a gtf or a gff file for the UU GSD1.0 annotation? I'm just not quite sure what to do with the text. Is it an input file for another piece of software?

Best,

Brian

[Daniel Schmelter]

Hello Brian,

There is not a GTF or GFF file associated with this annotation data. I cannot comment on whether or not it inputs into any pipelines. You can look at the source file where we got the data and see that it too is in BED format with a track line for the Genome Browser:

https://export.uppmax.uu.se/uppstore2017228/ucsc_cf4_annotation/UU_GSD1.0_gene_annotation.bed

If you want this data in GTF/GFF format, you can convert it using a two-step command-line utility process, bedToGenePred, and then genePredToGtf. These utility commands can be found in our utility downloads page for your operating system.

http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads

Alternately, you can get this data in GTF format using the Table Browser tool and selecting GTF output format in the dropdown. I made a session with those settings pre-filled below:

http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=canFam4.uuGeneGTF

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

On Fri, Mar 26, 2021 at 10:56 AM Brian Williams <bgwi...@ncsu.edu> wrote:

[Daniel Schmelter]

Hello Brian,

As it turns out, one of our engineers contacted the data author who just shared the following links for GTFs of these annotations. 

the original file is here:

https://export.uppmax.uu.se/uppstore2017228/b14/files_for_MS/UU_GSD1.0_annotation_june29_no_colon.gtf

And I have a file converted to gtf here:

UU_GSD1.0_annotation: 

https://export.uppmax.uu.se/uppstore2017228/b14/files_for_MS/UU_GSD1.0_annotation_june29_no_colon.gtf

And finally the new NCBI annotation in gtf format with ucsc-names for chromosomes:

GCF_011100685.1_UU_C: 

https://export.uppmax.uu.se/uppstore2017228/b14/files_for_MS/GCF_011100685.1_UU_Cfam_GSD_1.0_genomic.NameB614.gtf.ucsc.gtf

Best wishes,

Daniel Schmelter

[Brian Williams]

Hi Daniel, 

Thank you for the help. This is all great! I really appreciate one of your team members reaching out to the group and I really appreciate you explaining how to generate a GTF file. 

Thank you so much! You have been such a great help!!

Best,

Brian