- The pipeline failed to run if no INPUT are done. Following ENCODE guidelines, control experiment must be performed and are used during peak calling.
**What if I have one INPUT for one mark, and two for another ?**
-We advice to run 2 different analysis. Experimental design with different numbers of replicates for IP or INPUT is not included for now.
- Experimental design with different numbers of replicates for IP and/or INPUT are included to ChIPflow.
**What if I have one replicate for one mark ?**
- The pipeline will stop after peak calling, without selection of peaks as reproducibility cannot be ensure with only one replicate.
**What are the default ADAPTERS for cutadapt?**
- By default, TruSeq and NEBNext Kits for Illumina are done in the config/adapt.fa.
- By default, indexes from TruSeq and NEBNext Kits for Illumina are done in the config/adapt.fa.
**Can I give my own adapters list for cutadapt?**
- In-house adapters could be added to the config/adapt.fa or in an independent file. Don't forget to change the value of `adapter_list` in cutadapt rule in `config.yaml` file.
