Hello Felix, Is there any way to get the FourCSeq-Pipeline running without any replicates or samples under different conditions? I am setting up 4C-Seq and only have sequencing outputs without replicates so far. I tried doing FourCSeq with one of my sequence files and ran into following error during creation of the FourCobject:

Error in DESeqDataSet(SummarizedExperiment(colData = colData, metadata = metadata, : design has a single variable, with all samples having the same value. use instead a design of '~ 1'. estimateSizeFactors, rlog and the VST can then be used In addition: Warning message: In DESeqDataSet(SummarizedExperiment(colData = colData, metadata = metadata, : all genes have equal values for all samples. will not be able to perform differential analysis

I guess this has to do with singular samples without replicates. Thats why I tried it again (just for fun), this time by just copying one of the bam files and using that as replicate, but then I ran into a similar error when getting Z Scores. Is there any workaround for me or is there simply no way to use FourCSeq without replicates? I know, not having replicates will not generate meaningful data, but I want to see how the output from FourCSeq compares to other algorithms like 4Cker (which worked with singular samples by the way).

Thanks, Johannes