Query : rheSus Macaque rheMac8 assembly

[Sharma, Himanshu]

Hi,

I am finding below error in getting  KnownGenes information as mentioned in http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format

 

./genePredToGtf rheMac8 knownGene knownGene.gtf

Can't start query:

select * from knownGene

 

mySQL error 1146: Table 'rheMac8.knownGene' doesn't exist (profile=<noProfile>, host=genome-mysql.cse.ucsc.edu, db=rheMac8)

 

Could you please guide me the path of known_gene.txt dump ? Just like it is mentioned for hg19: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz

 

Also could you please guide me path for related chromosome fasta files of macaca mulata (rheMac8 Assembly) .

 

We really appreciate your help in the resolution.

 

Regards,

Himanshu

 

[Brian Lee]

Dear Himanshu,

Thank you for using the UCSC Genome Browser and your question about knownGene for rheMac8.

The rheMac8 browser does not include the knownGene table from the UCSC Genes Track as seen in hg19.

The available gene tracks and their corresponding description pages can be found from the following places:
- The rheMac8 Genome Browser at http://genome.ucsc.edu/cgi-bin/hgTracks?db=rheMac8, in the "Genes and Gene Predictions" Group, where the track names can be clicked which will lead to description pages:

1. Augustus Gene Predictions
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rheMac8&g=augustusGene

2. Genscan Genes
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rheMac8&g=genscan

3. NCBI RefSeq Genes
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rheMac8&g=refGene

Downloads for these data, including fasta files, can be found by accessing the blue horizontal menu bar > Downloads > Genome Data > Rhesus > rheMac8 Full Data Set: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/bigZips/
Parent directory: http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply toge...@soe.ucsc.edu. All messages sent to that address are 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
UCSC Genomics Institute

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