Downloading full gene annotations for RhesusBase genes
Question:
How can I download the full gene annotations for the RhesusBase genes from www.rhesusbase.org? I can see how to do bulk downloads of this information for Genes and Gene Prediction tracks, but the RhesusBase Genes are not listed under those tracks. The Gene Page does not seem to have the same functionality and would only give the start-stop positions of the genes versus the full intron-exon structure.
Response:
RhesusBase Genes track data are available on BioMart download page now. Please download from the portal.
Getting multiple alignment from RhesusBase
Question:
I hope to obtain multiple alignment and conservation score data from RhesusBase, but can't find where to get it.
Response:
6way and 9way multiple alignment and conservation score in MAF and
bigWig format can be downloaded by mailing RhesusBase team
.
Can't get information of certain gene on Gene Page
Question:
I want to get information about some genes, but got no hit from query by symbol
Response:
For scare and uncompleted annotations of macaque, some genes in rhesus aren't annotated with equivalent symbol as human but assigned as LOCNNNNN. To retrieve these genes in Gene Page, the location-based search offers a more general resolution. Location for these genes from other public resources, like UCSC, can be used to take location-based search in RhesusBase to hit these genes.
RhesusBase gene model data dump
Question:
I was interested in comparing your annotations against the Ensembl annotations. Is it possible to provide us with a data dump (if possible, in gff format) of the gene models (with exons, CDS, UTR annotations)?
Response:
The rheMac2 gene model in gff and other formats is available at Frequently-used Files
RhesusBase gene model translation
Question:
A number of the "new" RhesusBase annotated gene models, when translated seem to have a number of stop codons.
Response:
The "new" gene models in RhesusBase refer to de novo-assembled transcripts using Cufflinks (with RNA-seq sequencing reads as input). Actually a large proportion of these transcripts represent long-noncoding RNAs. We included these transcript in RhesusBase gene models in that the exon-intron structures of new these transcripts are reliable, instead of the coding potential.
RhesusBase transcript searching
Question:
I am having trouble locating many of the genes from the gff file in the RhesusBase database, when I am trying to do a comparison. For example, the two IDs (IMMRT10000146190 and IMMRT10000145774) do not show up when I did a search based on RhesusBase Transcript ID.
Response:
Although the gene models for these new transcripts were included in RhesusBase GFF file, they are absent in RhesusBase Gene Page. These transcripts may be found on RhesusBase Genome browser by location-based searching.