Mouse refLink.txt.gz

[Apurva Hegde]

Hi,

I was wondering how to download the mouse-equivalent for the human refLink.txt.gz and came across this post:

https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/reflink/genome/14OE9bLpIIE/7iGimRPab6IJ

However, when I try to follow these instructions for mouse, I don't see a "refLink" option in the "table" dropdown menu, for the Dec 2011 (GRCm38/mm10) version of the mouse genome.

1) Is there something I'm missing or does refLink.txt.gz not exist for the mouse genome?

2) Is there any documentation/description of what this file contains?

Regards,

Apurva Hegde

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[Brian Lee]

Delete

Dear Apurva,

Thank you for using the UCSC Genome Browser and your question about the refLink file.

You can access it from the hgFixed database, or also download a file version here: http://hgdownload.cse.ucsc.edu/goldenpath/hgFixed/database/refLink.txt.gz

Here is a note about the changes where in 2016 we moved this data to a centralized hgFixed database instead of replicating it in each database for each assembly: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download35

From the Table Browser you can access this file and also see information about the schema.

1. From http://genome.ucsc.edu, select "Tables" from the blue navigation 
bar at the top of the screen.

2. Select the following options: 
Clade: Mammal 
Genome: Mouse 
Assembly: mm10 
Group: All Tables
Database: hgFixed 
Table: hgFixed.refLink

Click "describe table schema" to see a table description. You can use the "identifiers" option to input a list with "paste list" or "upload list" if you know the items you want.

Or you can also access this information with MySQL queries: http://genome.ucsc.edu/goldenPath/help/mysql.html

mysql --user=genome --host=genome-mysql.soe.ucsc.edu -ANe 'select * from refLink where name like "SIRT1"\G' hgFixed

Example output
name: Sirt1
product: NAD-dependent protein deacetylase sirtuin-1 isoform 1
mrnaAcc NM_019812
protAcc NP_062786
geneName 41734
prodName 539633
locusLinkId 93759
omimId0

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further questions and reply to gen...@soe.ucsc.edumessages will be archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html
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