iGenome indexes for Chimpanzee and Bonobo (panTro3)
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7.6 years ago
biorepine ★ 1.5k

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.

bowtie tophat • 1.8k views
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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!

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

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7.6 years ago

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

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

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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).

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