diff --git a/README.md b/README.md index 8faeae9f3a379ce248a70c4e7f28f707846c917e..6cc1de247e573d60637687c181e210ced9d78984 100644 --- a/README.md +++ b/README.md @@ -499,10 +499,10 @@ done - 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 ?** -- 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 ?** -- 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 ?** - The pipeline will stop after peak calling, without selection of peaks as reproducibility cannot be ensure with only one replicate.