Missing Metadata for Signac Analysis #1612
Replies: 2 comments
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That step loads the metadata generated by cellranger. You can continue without it, bear in mind that the cellranger-generated metadata will not be present in your object |
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Hi, I have a similar problem. I was wondering what the cell ranger-generated metadata file looked like? I believe these are the output files: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-gex-overviewm but I cannot see which one could be the metadata file? I used cell ranger aggr for integration and the outputs are: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-aggr-outputs. However, again I cannot see which file could be the metadata. Thank you for your help. |
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Hi,
I am trying to perform scATAC analysis from two published data - but neither has metadata. One paper has barcodes.tsv.gz, matrix.mtx.gz, peaks.bed.gz, and fragments.tsv.gz. The other paper has fragments.tsv.gz, fragments.tsv.gz.tbi.gz, and filtered_feature_bc_matrix.h5 files.
Can I continue the analysis without running this step in the beginning?
metadata <- read.csv(
file = "../vignette_data/atac_v1_pbmc_10k_singlecell.csv",
header = TRUE,
row.names = 1
)
Many Thanks!
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