I am interested in using the FourCSeq pipeline for the analysis of some Capture-C data I have generated in replicate. One question I have is how to handle the situation where only one 4-bp cutter enzyme was applied (DpnII) and not two different enzymes like in standard 4C-seq applications. Do I enter the DpnII recognition sequence (GATC) twice for both reSequence1 and reSequence2?
Since Capture-C uses 160 bp biotinylated probes for capture vs an inverse PCR with primers, I assume it is okay to enter my probe sequence (1 of a possible 2) that identifies my viewpoint fragment?
Are there any other items that I need to take into consideration when either setting up this pipeline or interpreting the results for Capture-C data?
Look forward to your responses,