Can I run chip-seq-pipeline without input files?

[Reemann]

Describe the bug

If I run without chip.ctl* set in .json, it will report:

* Error: SPP requires control inputs. Define control input files (chip.ctl_*) in an input JSON file.

I know tf mode runs with input files which is different from histone mode, but is there any possibility to run ChIP-seq-pipeline without input files? Because I don't have input datasets in my research.

OS/Platform

• OS/Platform: Ubuntu
• Conda version: conda 4.10.3
• Pipeline version: [e.g. v1.6.0]
• Caper version: [e.g. v1.2.0]

Input JSON file

{
    "chip.pipeline_type" : "tf",
    "chip.genome_tsv" : "./genome_ENCODE/hg38.tsv",
    "chip.fastqs_rep1_R1" : ["./0_raw_data/TF1_rep1_R1.fastq.gz"
    ],
    "chip.fastqs_rep1_R2" : ["./0_raw_data/TF1_rep1_R2.fastq.gz"
    ],
    "chip.paired_end" : true,
    "chip.title" : "TF1",
    "chip.description" : "TF1"
}

Troubleshooting result

Paste troubleshooting result.

* Error: SPP requires control inputs. Define control input files (chip.ctl_*) in an input JSON file.

[leepc12]

I think you can try with macs2 peak caller. Please add the following to your input JSON and try again. This will change your peak caller from spp to macs2. spp always requires inputs but macs2 doesn't.

{
    "chip.pipeline_type": "tf",
    "chip.peak_caller": "macs2"
}

[Reemann]

I'll try as you recommend. Thanks a lot!

[Kmrouj]

Hello all,
I'm facing the same issue (also running a 'tf' chip). I was wondering whether adding macs2 (instead of spp) did help solve the issue.
Also, I wanted to know where exactly in the JSON file we should add "chip.peak_caller": "macs2" toward the end or just after "chip.pipeline_type": "tf".

Thanks.

Best,
Karim