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biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
http://bioepic.readthedocs.io
MIT License
31 stars 6 forks source link

Genome request #65

Closed sejmodha closed 6 years ago

sejmodha commented 6 years ago

Hi There,

I am trying to use epic for ChiPSeq data for a genome that does not exist in the current list of the available genomes. It is possible to use epic in such cases?

Genome PbergheiANKA not found
If yours is not there, please request it at github.com/endrebak/epic . (File: genomes, Log level: ERROR, Time: Tue, 31 Oct 2017 15:21:05 )

I would like to request the Plasmodium genome be added to the list.

Thanks

endrebak commented 6 years ago

Yes, you can use the —chromsizes flag and the —effective genome size flag together to use whatever genome. Does the plasmodium genome have a UCSC code, like hg19 for human? If not I need to think a bit about how to add it.

endrebak commented 6 years ago

Thanks for the request btw.

sejmodha commented 6 years ago

Thanks for the clarification, I have managed to run epic with the custom genome. I am not sure if UCSC code exists for this particular genome.

Thanks for your help once again.

endrebak commented 6 years ago

Super! The egs should just change how many regions are diff enriched, so it does not matter that much. The most interesting regions will always be the lowest fdr.

On Wednesday, November 1, 2017, sejmodha notifications@github.com wrote:

Thanks for the clarification, I have managed to run epic with the custom genome. I am not sure if UCSC code exists for this particular genome.

Thanks for your help once again.

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