Chip-seq single cell

[A-legac45]

Hello everybody,

I am trying to use ArchR to analyse a dataset of sc chip-seq for specific histone marks. Is that possible? Does other tools can be used ?

I am encountering the two following problems with ARCHR :

1. If yes I do not get why if I put by default like this the code I get different clusters

proj1 <- addIterativeLSI(ArchRProj = proj1, useMatrix = "TileMatrix", name = "IterativeLSI3")

proj1 <- addClusters(input = proj1, reducedDims = "IterativeLSI3", force = TRUE)

2. and If I look to the parameters and try to improve I get only one cluster

proj1 <- addIterativeLSI(
ArchRProj = proj1,
useMatrix = "TileMatrix",
name = "IterativeLSI",
iterations = 2,
clusterParams = list( #See Seurat::FindClusters
resolution = c(0.2),
sampleCells = 10000,
n.start = 10
),
varFeatures = 25000,
dimsToUse = 1:30, force = TRUE
)

proj1 <- addIterativeLSI(
ArchRProj = proj1,
useMatrix = "TileMatrix",
name = "IterativeLSI2",
iterations = 2,
clusterParams = list( #See Seurat::FindClusters
resolution = c(0.1, 0.2, 0.3, 0.4, 0.5, 2)
),
varFeatures = 20000,
dimsToUse = 1:30, force = TRUE
)

proj1 <- addClusters(input = proj1, reducedDims = "IterativeLSI", method = "Seurat",
name = "Clusters", resolution = 0.8, force = TRUE)

[rcorces]

sc ChIP-seq is not a supported use case for ArchR and we dont have bandwidth to help troubleshoot related errors. Sorry to not be able to help on this.