I think that I already prepare all data sets but it didn't work. Please help me. I don't know what's wrong.
(ps) barcodes.tsv.gz & genes.tsv.gz & matrix.mtx.gz are unzip files
•
written
by
kayah •
1 answer
What version of cellranger is this data from?
As the seurat manual says:
# For output from CellRanger < 3.0
data_dir <- 'path/to/data/directory'
list.files(data_dir) # Should show barcodes.tsv, genes.tsv, and matrix.mtx
expression_matrix <- Read10X(data.dir = data_dir)
seurat_object = CreateSeuratObject(counts = expression_matrix)
# For output from CellRanger >= 3.0 with multiple data types
data_dir <- 'path/to/data/directory'
list.files(data_dir) # Should show barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz
data <- Read10X(data.dir = data_dir)
seurat_object = CreateSeuratObject(counts = data$`Gene Expression`)
seurat_object[['Protein']] = CreateAssayObject(counts = data$`Antibody Capture`)
You appear to have files named for older cellranger data but they are not from that version?
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.
Also unless you have a very good reason to be using that old a version of CellRanger, I'd really recommend a newer one. Newer versions will do a much better job with cell filtering and generally utilize more reads in counts (as CellRanger 7+ will include intronic reads by default), resulting in more usable cells recovered.
Log in to answer this question.
-
Is it possible to see so little adipocyte in white adipose tissue?
written by kayah •
-
singlecell annotation
written by kayah •
-
compare dimplot(single cell)
written by kayah •
-
Is there anyone who downloaded Azimuth packges?
written by kayah •
-
how to convert SummarizedExperiment files to DESeqDataSet??
written by kayah •
-
single cell RNA seq integration(Error in UseMethod(generic = "as.sparse", object = x))
written by kayah •
-
KEGG analysis in Hordeum
written by martta95 •
-
Error in DiffBind
written by Scabbards •
-
[Errno 2] No such file or directory: '0-rawreads' when I run Falcon unzip with hifi data
written by Feng •
-
How can I add text label outside the tree in iTOL ?
written by anran04100 •
Please write professionally on professional forums. Avoid IM/SMS jargon such as "plz" and multiple dots (Example: "plz help me..." should be "Please help me.") I've fixed things for you this time.