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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

Can we run Epic without a control file? #62

Closed CodeInTheSkies closed 6 years ago

CodeInTheSkies commented 7 years ago

Hi there,

I have ChIP data for H3K27me3, but the biologist did not do a ChIP control experiment. So, I don't have a matching control file. When I tried to run epic, it crashed and threw an error saying it requires a control file.

Is it not possible at all to run epic without a control file?

I searched online, and for histone marks, many people say epic (SICER) is better, although MACS 2 seems to also have the ability to process broad peaks, possibly histone marks.

Anyway, please let me know if I can still run epic without controls. Otherwise, I think I have no choice but to go for MACS?

Thanks a lot!

endrebak commented 7 years ago

You need to use macs2 :)

On Thursday, August 3, 2017, CodeInTheSkies notifications@github.com wrote:

Hi there,

I have ChIP data for H3K27me3, but the biologist did not do a ChIP control experiment. So, I don't have a matching control file. When I tried to run epic, it crashed and threw an error saying it requires a control file.

Is it not possible at all to run epic without a control file?

I searched online, and for histone marks, many people say epic (SICER) is better, although MACS 2 seems to also have the ability to process broad peaks, possibly histone marks.

Anyway, please let me know if I can still run epic without controls. Otherwise, I think I have no choice but to go for MACS?

Thanks a lot!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/epic/issues/62, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0rGLWYR3sGmbricKQNKsNuMhMCGsks5sUfnHgaJpZM4OstSa .

endrebak commented 7 years ago

Or the original sicer... Google sicerpy

On Friday, August 4, 2017, Endre Bakken Stovner endrebak85@gmail.com wrote:

You need to use macs2 :)

On Thursday, August 3, 2017, CodeInTheSkies <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

Hi there,

I have ChIP data for H3K27me3, but the biologist did not do a ChIP control experiment. So, I don't have a matching control file. When I tried to run epic, it crashed and threw an error saying it requires a control file.

Is it not possible at all to run epic without a control file?

I searched online, and for histone marks, many people say epic (SICER) is better, although MACS 2 seems to also have the ability to process broad peaks, possibly histone marks.

Anyway, please let me know if I can still run epic without controls. Otherwise, I think I have no choice but to go for MACS?

Thanks a lot!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore-ntnu/epic/issues/62, or mute the thread https://github.com/notifications/unsubscribe-auth/AQ9I0rGLWYR3sGmbricKQNKsNuMhMCGsks5sUfnHgaJpZM4OstSa .