Dear Dr. Stuart,
Thank you for developing this amazing tool!
I'm analyzing a scATAC-seq dataset following this tutorial: https://satijalab.org/signac/articles/pbmc_vignette.html
An error occurred from CreateChromatinAssay:
chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-"),
genome = 'hg19',
fragments = 'Myfragments.tsv.gz',
min.cells = 10,
min.features = 200
)
Computing hash
Checking for 7840 cell barcodes
Error in SetAssayData.ChromatinAssay(object = new.assay, slot = "ranges", :
Number of ranges provided is not equal to the number
of features in the assay
Since I did not provide "ranges", genomic ranges should be extracted from the row names of matrix and the number of ranges should be equal to the number of features. ("A set of genomic ranges must be supplied along with the matrix, with the length of the ranges equal to the number of rows in the matrix. If a set of genomic ranges are not supplied, they will be extracted from the row names of the matrix.").
Could you please explain a little bit why this error occurred? Any suggestions?
Thanks,
Mao
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