Question regarding rn6 assembly
Arghavan Ashouri
Jonathan Casper
Hello Arghavan,
Thank you for your question about the availability of the Ensembl genes track on the rn6 genome assembly. While we may add an Ensembl Genes track to the rn6 assembly, there are no plans for it right now. We do have plans to add a track containing genes from the Rat Genome Database (RGD - http://rgd.mcw.edu/), but there is no timetable for when that track will be available.
One of our engineers suggests that you could try lifting the Ensembl Genes track (table ensGene) from rn5 to rn6 to get some approximate gene names. One way to go about this would be to follow these steps:
1. Visit the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables.
2. Select the following options:
Clade: Mammal
Genome: Rat
Assembly: Mar. 2012 (RGSC 5.0/rn5)
Group: Genes and Gene Predictions
Track: Ensembl Genes
Table: ensGene
Region: genome
Output Format: BED - browser extensible data
Output File: ensGene_from_rn5.bed
3. Click "get output".
4. On the next page, leave the default setting to create "one BED record per whole gene" and click "get BED".
5. Your computer should now download a file titled "ensGene_from_rn5.bed". The next step is to load this into the LiftOver tool for conversion to the rn6 assembly.
6. Browse to the LiftOver tool at http://genome.ucsc.edu/cgi-bin/hgLiftOver (also available in the top menu under "Tools").
7. Select the rat rn5 assembly as the "Original Assembly" and rat rn6 as the "New Assembly".
8. Click the "choose file" button and select the "ensGene_from_rn5.bed" file that you previously downloaded. Click "submit file".
9. In the Results section, there should be a link to "View Conversions". Click that link to download a BED file that contains the coordinates of the ensGene track as lifted to the rn6 genome.
10. Open the Custom Track tool at http://genome.ucsc.edu/cgi-bin/hgCustom.
11. If you already have other custom tracks loaded, you will need to click on the "add custom tracks" button. Otherwise, proceed to step 12.
12. Select the rat rn6 genome assembly at the top of the "Add Custom Tracks" page, then click the top "Choose File" button (next to "Paste URLs or data") and select the file of lifted coordinates that you downloaded in step 9.
13. Click "submit".
You should now have a custom track loaded for the rn6 genome assembly that contains an automatic conversion of the Ensembl genes track from rn5. Please note that as this is an automated conversion, it will not have gone through the same examination and testing that our standard track releases do. It may still be enough, however, to provide you with the gene names that you are looking for.
Please note that there are additional options available when configuring the LiftOver tool. We recommend that you use the default values to start, but you are welcome to experiment with the settings if you prefer. The input file from step 5 should be in BED 12 format, so all of the options should be available.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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Thibaut Hourlier
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