read10xCounts for Cell Ranger 7 Output
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Entering edit mode
Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 1 day ago
Australia

It seems only Cell Ranger versions 2 and 3 are supported: version = c("auto", "2", "3"). How about 7.0.1?

> dir
[1] "DANFRO_CUL1HNM3"
allCounts <- read10xCounts(dir)
  .check_for_compressed(barcode.loc, compressed): cannot find 'DANFRO_CUL1HNM3/barcodes.tsv' or its gzip-compressed form

The folder structure looks like

$ ls DANFRO_CUL1HNM3
DANFRO_CUL1HNM3.mri.tgz  SC_RNA_COUNTER_CS  _cmdline  _filelist  _finalstate  _invocation  _jobmode  _log  _mrosource  _perf  _sitecheck  _tags  _timestamp  _uuid  _vdrkill  _versions  outs
$ ls DANFRO_CUL1HNM3/outs
analysis       filtered_feature_bc_matrix     metrics_summary.csv  possorted_genome_bam.bam      raw_feature_bc_matrix     web_summary.html
cloupe.cloupe  filtered_feature_bc_matrix.h5  molecule_info.h5     possorted_genome_bam.bam.bai  raw_feature_bc_matrix.h5
DropletUtils • 855 views
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Entering edit mode
@jonathan-griffiths-20559
Last seen 3 months ago
Cambridge UK

You need to look in the filtered_feature_bc_matrix or raw_feature_bc_matrix folders for those files.

Jonny

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