Unable to get known Canonical track for GENCODE v34

[Genetics Savvy]

Hi team,

I have tried downloading knownCanonical track for All Gencode v34, but unable to get the knowCanonical track for All Gencode v34, however, it is there for track GENCODE v32. Is there any way to download knownCanonical data for track  All Gencode v34?

Steps I did for downloading the knownCanonical data for older version:

Choose:

clade: Mammal

genome: Human

assembly: Dec 2013 (GRCh38/hg38)

group: Genes and Gene Predictions

track: GENCODE v32

table: KnownCanonical

region: genome

output format: selected fields from primary and related tables

output file: GRCh38_UCSC_ensembl_canonica.txt

Select kgXref and knownToEnsembl from Linked Tables then click on allow selection from checked tables

Select transcript from hg38.knownCanonical, geneSymbol from hg38.kgXref fields and value from hg38.knownToEnsembl table.

Now click get output and save the file

Thanks and Regards,

Savvy

[Jairo Navarro Gonzalez]

Hello,

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

While we do not have this data set available in the Table Browser, one of our engineers has created a subset of the known Canonical track for GENCODE v34. The dataset can be found at the following location:

https://hgwdev-braney.gi.ucsc.edu/~braney/knownCanonicalV34.txt

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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[Genetics Savvy]

Hi Jairo Navarro, 

Though we can use the dataset that you have provided to us, would it be possible to have a two column dataset where we have the gene name and the corresponding canonical transcript? 
something like this: 

C1orf141 ENST00000371007.6

PKP1 ENST00000367324.7

RERE ENST00000400908.7

CSMD2 ENST00000373388.6

thanks,

savvy

[Daniel Schmelter]

Hello Savvy,

Thanks for your interest and specificity.

We are happy to provide you with such a file. You can access it at the following link:

https://hgwdev.gi.ucsc.edu/~braney/gencodeV34CanonWSym.txt

We wish you the best with your investigations! If you have any further questions or comments, please reply-all so that our whole support team can see your message.

Warmly,
Daniel Schmelter
UCSC Genome Browser

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAFx6sdg4LQUwMXmq-yzDXR_%3D7sTLbNf%2By%3DrpzwyqQeaMqrW7dg%40mail.gmail.com.