- First INPUT could be used for peak calling on all IP to reduce technical variability, but each IP could be associated to a specific INPUT in the design file.
- First INPUT could be used for peak calling on all IP to reduce technical variability, but each IP could be associated to a specific INPUT in the design file.
**What if I have no INPUT ?**
**What if I have no INPUT ?**
-The pipeline failed to run if no INPUT are done. Following ENCODE guidelines, control experiment must be performed and are used during peak calling.
- Following ENCODE guidelines, control experiment must be performed and are used during peak calling for ChIp-seq experiments. Nevertheless, the CUT&Tag method reduces the background noise and allows for more precise and sensitive detection of protein-DNA interactions, reducing the need for an input control or IgG control. Follow the CUT&Tag section for more explanation about running ePeak without INPUT.
**What if I have one INPUT for one mark, and two for another ?**
**What if I have one INPUT for one mark, and two for another ?**
- Experimental design with different numbers of replicates for IP and/or INPUT are included to ChIPflow.
- Experimental design with different numbers of replicates for IP and/or INPUT are included to ePeak.
**What if I have one replicate for one mark ?**
**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.
- The pipeline will stop after peak calling, without selection of peaks as reproducibility cannot be ensure with only one replicate.
