iGenome indexes for Chimpanzee and Bonobo (panTro3)

Question

[biorepine]

Dear Biostars,

I am trying to map Chimpanzee and Bonobo RNA-Seq reads against their genomes by using TopHat. Do you know where can I find the indexes of these genomes ? thanx in advance.

[sara.linker]

Have you been able to resolve mapping to the bonobo genome? I'm trying to do the same thing and haven't found a good reference genome to start with. I have seen some people map to PanTro4 instead. Any help would be much appreciated! Thanks!

[biorepine]

I haven't started building. Probably will start building them end of this month. Would you like to join along with me @sara?

Answer 1

[Devon Ryan]

The chimp index is available from iGenomes. You might have to build the bonobo one yourself (it's not difficult).

[biorepine]

thanx. So how can I build bonobo index ? :P

[Devon Ryan]

Tophat uses indices made by bowtie2, so just read through the help for bowtie2-build. You'll need a copy of the reference genome and a bit of time (it's just one command, but it takes a while to run).