Number of cell types required

[lucygarner]

How many cell types are required for haystack_bio to provide accurate and reliable results? For example, I have ATAC-seq and RNA-seq data on three cell types? Would this be sufficient for running haystack_bio?

[rfarouni]

Should be sufficient. That said, at one step of the pipeline a measure of signal variability is computed to determine the hotspot regions, but with a small sample size (e.g. 3), the variance of this variability measure is high, so I would chose a more conservative threshold to select them.