Running Cistopic
Sayyam-Shah opened this issue · 1 comments
Hello @cbravo93,
I am interested in using cistopic, however, I am experiencing some problems as I am more used to RNA seq data.
I am creating the cistopic object below.
matrix <- BM77@assays$ATAC@counts
rownames(matrix) <- sub('-', ':', rownames(matrix))
cisTopicObject <- createcisTopicObject(count.matrix = matrix)
However, I get an error upon running the runWarpLDAModels method.
cisTopicObject <- runWarpLDAModels(cisTopicObject, topic=c(7:17), seed=987, nCores=20, iterations = 100, addModels=FALSE)
[1] "The number of cores (20) is higher than the number of models (11)."
[1] "Exporting data..."
[1] "Run models..."
Error in serialize(data, node$con) : error writing to connection
How may I debug the error? Would you recommend I move over to pycistopic? Personally, I am better at python than R. To create a cistopic object with pycistopic, do we just need to feed in the regions bed file, fragments.tsv.gz file, and metrics? What does the metrics file look like (ex. A column named cell_barcode)? What are blacklist and valid_bc files?
Sorry, I am new to ATAC analysis.
Hi!
Can you try lowering the number of cores? cisTopic is deprecated, I'd suggest indeed to move to pycisTopic. You have plenty of tutorials to follow at: https://pycistopic.readthedocs.io/en/latest/
Good luck!
C