Thank you for the prompt response! Even with that fix I am still getting an error:
Error in CreateFragmentObject(path = fragments, cells = cells, validate.fragments = validate.fragments, :
Fragment file is not indexed.
I am trying to follow the tutorial for Signac 1.10.0... I am getting an error when it comes to the part of the code "create ATAC assay and add it to the object" below is the code that I am running
counts <- Read10X_h5("~/Documents/multiomic/pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5")
fragpath <- "../Documents/multiomic/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz"
annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevels(annotation) <- paste0('chr', seqlevels(annotation))
pbmc <- CreateSeuratObject(counts = counts$`Gene Expression`,assay = "RNA")
The above code runs fine, but the code below is where I get an error:
pbmc[["ATAC"]] <- CreateChromatinAssay(counts = counts$Peaks,sep = c(":", "-"),fragments = fragpath,annotation = annotation)
This is the error I am getting:
Error in CreateFragmentObject(path = fragments, cells = cells, validate.fragments = validate.fragments, :
Fragment file does not exist.
I am assuming it has something to do with the path that I am setting... If someone could please provide insight to the correct way to set path I would appreciate it. I am currently using the atac_fragments.tsv.gz file that I am setting my path to.
Presumably a typo since you have:
counts <- Read10X_h5("~/Documents/multiomic/pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5")
But then:
fragpath <- "../Documents/multiomic/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz"
Which should probably be:
fragpath <- "~/Documents/multiomic/pbmc_granulocyte_sorted_10k_atac_fragments.tsv.gz"
Gotta pay real close attention when providing file paths.
Thank you for the prompt response! Even with that fix I am still getting an error:
Error in CreateFragmentObject(path = fragments, cells = cells, validate.fragments = validate.fragments, :
Fragment file is not indexed.
Log in to answer this question.