hg19 rnaGene and mrna download

[Paula Beati]

Hello,

I need to download hg19 tracks equivalent to these:

clade: Mammal
genome: Human
assembly: NCBI36/hg18
group: Genes and Gene Prediction
track: RNA Genes
table: rnaGene

clade: Mammal
genome: Human
assembly: NCBI36/hg18
group: All Tables
database: hg18
table: mrna

Can you provide me with those links?
Or tell me how to find these tracks in Table Browser hg19 assembly?

Thanks in advance,
Paula.

[Matthew Speir]

Hello, Paula.

Thank you for your question about downloading data from the UCSC Genome Browser.

You can find the downloads of complete tables on our downloads server, http://hgdownload.soe.ucsc.edu/downloads.html, in the section of the assembly you're interested under the "Annotation database" link.

For hg19, there is no RNA Genes track and thus no rnaGene table. The non-coding RNA annotations are spread across a few different tracks from a few different sources:

• sno/miRNA: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgRna
• tRNAs: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=tRNAs
• GENCODE Pseudogenes: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV19

I'm not sure that the combination of all of these tracks is equivalent to the hg18 rnaGene table as they were likely produced by different methods.

You can find downloads for these tables in hg19 as well as the "mrna" table on our download server:

• mrna: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/all_mrna.txt.gz
• sno/miRNA: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz
• tRNAs: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/tRNAs.txt.gz
• GENCODE Pseudogenes: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodePseudoGeneV19.txt.gz

If these three additional tracks don't meet your needs as far as RNA genes go, you may want to look into using LiftOver to convert the annotation coordinates from hg18 to hg19. You can use the web interface for LiftOver: https://genome.ucsc.edu/cgi-bin/hgLiftOver or you can download the command-line utility from our download server, http://hgdownload.soe.ucsc.edu/admin/exe/, along with the hg18 to hg19 liftOver file, http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.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.

Matthew Speir

UCSC Genome Bioinformatics Group

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