--macs2-string parameter: can I use --control?

[vidaletal]

Thank you again for this tool,

I'm trying to use the MACS2 parameter --control using Hi-C as input.
However, I'm unsure how to proceed with the command to have the same effect as it has on regular ChIP-seq.

Can you please help me?
What would be the input in this case? Would be the .validpairs of the Input?

Thank you for your time.

[caleblareau]

Hi, So we’ve added support for the ‘control’ sample under limited circumstances now to evaluate things. One of these facets is that you have to pre-define your peak set (rather than calling them via macs2). I’d recommend figuring out what peaks you want to use with the treated sample only and then subsequently running those peaks as input with the control sample analysis.

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On Jan 28, 2020, at 9:33 AM, Raphael ***@***.***> wrote: Thank you again for this tool, I'm trying to use the MACS2 parameter --control using Hi-C as input. However, I'm unsure how to proceed with the command to have the same effect as it has on regular ChIP-seq. Can you please help me? What would be the input in this case? Would be the .validpairs of the Input? Thank you for your time. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#80?email_source=notifications&email_token=AD32FYN3NBUBFPOPI6UKO6TRAA63TA5CNFSM4KMTOOS2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IJHWIGQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD32FYJNXGM2HPEOSFJRO5LRAA63TANCNFSM4KMTOOSQ>.

[vidaletal]

Hi Caleb,

Many thanks for your prompt reply.
However, it was not clear which and how to use the arguments to this end in the command.
How it should be? Like the example below?

hichipper -o /foo/hichipper_SMC_peaks --macs2-string --control /foo/SMC_ChIPseq/MACS2/Input_ChIPseq.bed -ma 5000000 -mu /foo/hichipper_SMC.yaml

with the following hichipper_SMC.yaml:

peaks:
  - /foo/SMC_ChIPseq/MACS2/SMC_ChIPseq_peaks.bed
resfrags:
  - /foo/DpnII_resfrag_hg19.bed
hicpro_output:
  - /foo/HiCPro_dir

Or should I run the command with the .yaml file above?

hichipper -o /foo/SMC_peaks -ma 5000000 -mu /foo/hichipper_SMC.yaml

And then, from the output of the hichipper from the SMC HiChIP data set, I used its peaks for its Hi-C/ Input in the command plus the .yaml below?

hichipper -o /foo/Input_peaks -ma 5000000 -mu /foo/hichipper_Input.yaml

peaks:
  - /foo/HiChIP/hichipper/hichipper_SMC_peaks.bed
resfrags:
  - /foo/DpnII_resfrag_hg19.bed
hicpro_output:
  - /foo/HiCPro_dir

hichipper, version 0.7.7

thanks

Raphael