annotation database SQL table dumps for T2T-CHM13/hs1

[Edmonson, Michael]

Hi, I’m looking for genome annotation database SQL table dumps for T2T-CHM13/hs1, similar to those found for earlier genomes such as hg38.  For example the “ncbiRefSeq” table for hg38 can be found here:

 

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz

 

https://hgdownload.soe.ucsc.edu/downloads.html#human shows some resources for T2T-CHM13/hs1 under https://hgdownload.soe.ucsc.edu/goldenPath/hs1/, but apparently not the database export.  The genome browser does show gene annotations though, and poking around in the table browser I found something similar-ish in gddb: https://hgdownload.soe.ucsc.edu/gbdb/hs1/ncbiRefSeq/.

 

Are the SQL table annotations available anywhere?  These are incredibly useful and I’d love to have them for hs1.

 

Thanks,

Michael Edmonson

St. Jude Children’s Research Hospital

 

---

Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer

[Jairo Navarro Gonzalez]

Hello,

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

You may be interested in the GTF file for the NCBI RefSeq track on hs1. You can download this file using the following URL:

https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/genes/hs1.110.20220412.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

--

---
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/BN0PR04MB7952952C96AE3469971D9170E1E6A%40BN0PR04MB7952.namprd04.prod.outlook.com.

[Jairo Navarro Gonzalez]

Hello,

Thank you again for using the UCSC Genome Browser.

We have recently released a genePred format of the NCBI RefSeq track for hs1 that might be more of what you were looking for:

https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/genes/hs1.ncbiRefSeq.gp.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