Closed x811zou closed 5 years ago
Sounds like you're using 10x data. Read here: https://cole-trapnell-lab.github.io/cicero-release/docs/#loading-10x-scatac-seq-data for information on loading data from 10x outs
@hpliner I did read that part, but the input_cds from the below step is not a data frame but a dgMatrix and it does not contain the (Peak Cell Count), whereas, "cicero_data" is a data frame for atac-seq trajectory process.
input_cds <- input_cds[Matrix::rowSums(exprs(input_cds)) != 0,]
Most of Cicero's functions only use a CDS object like input_cds. The part of the tutorial using cicero_data is only there to show how to make your input_cds to begin with. Is there some function that you need the sparse matrix format (peak, cell, count) for? Or is there a function that's erroring out when you use the input_cds generated from your 10x output?
Hi, I want to load 10X scATAC-seq data ( matrix.mtx, features.tsv, and barcode.tsv) to Cicero in order to calculate co-accessibility. Is there any way to do that? I am following this link: https://cole-trapnell-lab.github.io/cicero-release/docs/#loading-10x-scatac-seq-data , but I have this errors that say the dimnames are not equal for peakinfo and indata.
Thanks!
Hello, you should be able to load your data using the monocle3 function designed for that:
cds <- load_mm_data(mat_path = "~/Downloads/matrix.mtx",
feature_anno_path = "~/Downloads/features.tsv",
cell_anno_path = "~/Downloads/barcodes.tsv")
Just be sure you're also using the monocle3 version of cicero (install instructions here: https://cole-trapnell-lab.github.io/cicero-release/docs_m3/#installing-cicero)
input_cds <- make_atac_cds(cicero_data, binarize = TRUE)
I noticed that the example data "cicero_data", has three columns. Peak Cell Count 140 chr18_30209631_30210783 AGCGATAGGCGCTATGGTGGAATTCAGTCAGGACGT 4 150 chr18_45820294_45821666 AGCGATAGGTAGCAGCTATGGTAATCCTAGGCGAAG 2 185 chr18_32820116_32820994 TAATGCGCCGCTTATCGTTGGCAGCTCGGTACTGAC 2 266 chr18_41888433_41890138 AGCGATAGGCGCTATGGTGGAATTCAGTCAGGACGT 2
Just wanna know how do you prepare this input data. I know that I could obtain Peak from peaks.bed and cell from barcodes.tsv and count from count matrix. However, they have different dimensions. How do you combine them to generate this input data? I am getting confused.
Thanks!