14 December, 2010

Beds, Wigs, BAMs and Variants for Flies, Rust, Aphids and 301 other species

Now that Ensembl Genomes has moved onto the 60 code base, all the goodies in Ensembl's user data site are available across all 304 species in Ensembl genomes - from tiny bacteria to crazy big plants.

One of these is uploads of BAMs, Wigs, Beds in the location based view. For example, if you have the following file to specify a SNP in Drosophila

2L 356013 356013 C/T

By using the Variant Effect Predictor, accessible from Tools on the top of each page, or the 'Manage your data' link at the left of pages, one can get the effect (synonymous, non synonymous, in a UTR etc) for the variant.

(You click on "Variant Effect Predictor", upload a text file of chr, position, allele and hit go) This can also be run as script using the API (the database is internet accessible so you just need to have an internet connection, Perl, MySQL client libraries and the Ensembl code base installed).

In addition, the full set of visualisation tools for your own data is also now accessible for all Ensembl Genomes species. For example, this bedGraph file:

track type=bedGraph name="BedGraph Format" description="BedGraph format" priority=20
2L 21302000 21302300 -1.0
2L 21302300 21302600 -0.75
2L 21302600 21302900 -0.50
2L 21302900 21303200 -0.25
2L 21303200 21303500 0.0
2L 21303500 21303800 0.25
2L 21303800 21304100 0.50
2L 21304100 21304400 0.75

Will render a nice little variable height picture in the main contigview display. Other options are available (like Bed and Wig format) - many of which people will know from UCSC. Come, try it out, and give us feedback at helpdesk@ensembl.org

No comments: