Enquiry : Annotation File for rhesus Macaque Assembly 8.0.1

[Sharma, Himanshu]

Hi ,

   I am working rhesus Macaque related RNA sequencing.

 

Could you please suggest the rhesus Macaque(Macaca Mulata) v8.0.1 genome fasta and respective annotation (GTF/GFF) files location?

 

I see the below path is dedicated for genome fasta ,but can’t find the respective GTF file.

 

http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/bigZips/

 

 

Please suggest.

 

Thanks,

Himanshu Sharma

 

IS System Programmer

Center for Vaccines and Immunity

Nationwide Children’s Hospital

Columbus OHIO

[Brian Lee]

Dear Himanshu,

Thank you for using the UCSC Genome Browser and your question about obtaining files for rhesus Macaque(Macaca Mulata) v8.0.1 or rheMac8.

On the Gateway page for an assembly, http://genome.ucsc.edu/cgi-bin/hgGateway?db=rheMac8, you can find links to the source information.

For example there is a link to "GenBank accession ID: GCF_000772875.2", which relates back to the original source:ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Macaca_mulatta/latest_assembly_versions/GCF_000772875.2_Mmul_8.0.1.

You can also find links to our own download resources: http://hgdownload.cse.ucsc.edu/downloads.html#rhesus

Under the "Full data set" link you will find the fasta information you were describing in your email:http://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/bigZips/

Under the "Annotation database" link you will find information for all the track data such as the refGene.txt.gz file which represents the RefSeq track:http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rheMac8&g=refGene

UCSC does not have GTF/GFF formats, but with the RefSeq track (refGene.txt.gz file) you can access the Gene Prediction (genePred) table format,http://genome.ucsc.edu/FAQ/FAQformat.html#format9, that is used to build this gene track where RefSeq RNAs (available in fasta as refMrna.fa.gz in the original "Full data set" directory) were aligned against the rhesus genome using BLAT.

We do provide tools that can convert Gene Prediction format to GTF, specifically genePredToGtf available precompiled in the appropriate directory here: http://hgdownload.cse.ucsc.edu/admin/exe/

Please review our archived mailing list of answers for more details about using genePredToGtf: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!search/genepredtogtf

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead togeno...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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