Dear sir, Kindly add reference Genome of Chicken (Gallus gallus) and Duck (Anas platyrhynchos) in Tophat Reference genome section.
Hello,
Tophat now has several of the most recent Chicken builds from UCSC added. Named like galGal3 (with variants), galGal4. Source UCSC main server, from Downloads: http://genome.ucsc.edu.
I found Duck (anaPla1) at the UCSC test browser http://genome-test.cse.ucsc.edu. It may or may not be fully published to their main server. Still, I'll add this to the list of genomes to add next (we can usually obtain the test-only data): Mallard duck Apr 2013 (BGI_duck_1.0/anaPla1)
To track progress, see this ticket. The genome is in the list of the (currently) second to last post. https://github.com/galaxyproject/galaxy/issues/1470
A custom genome is how to use the Duck (anaPla1) data right now. It may be a month at least before this is retrieved, indexed, and added to http://usegalaxy.org by us. Contact UCSC to find out how to gain public access to the anaPla1 genome fasta file for your own upload into a Galaxy history. https://wiki.galaxyproject.org/Support#Custom_reference_genome
Thanks! Jen, Galaxy team
Related: Addding iGenomes inGalaxy