Can't find metrics_summary.csv - hardcoded search dir

[mcsimenc]

I have the results from several cellranger count runs that are not in the cellranger output directory structure, for example:

.
.
├── CM_P2
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   ├── matrix.mtx.gz
│   └── metrics_summary.csv
├── CM_P3
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   ├── matrix.mtx.gz
│   └── metrics_summary.csv
.
.

It looks like where importCellRanger looks for metrics_summary.csv is hardcoded in importCellRanger.R:

metrics_summary <- .importMetricsCellRanger(samplePaths, sampleNames, "outs", "metrics_summary.csv")

Is there another way to get the summary into the SCE object with the singleCellTK API?

[mingl1997]

Hello,

We will change the function in a future update to support non-standard CellRanger output directories. For now, the workaround is to structure your directory as follows:

├── CM_P2
│    ├── outs
│    │     ├── raw_feature_bc_matrix
│    │     │     ├── barcodes.tsv.gz
│    │     │     ├── features.tsv.gz
│    │     │     ├── matrix.mtx.gz
│    │     ├── filtered_feature_bc_matrix
│    │     │     ├── barcodes.tsv.gz
│    │     │     ├── features.tsv.gz
│    │     │     ├── matrix.mtx.gz
│    └── metrics_summary.csv
├── CM_P3
│    ├── outs
│    │     ├── raw_feature_bc_matrix
│    │     │     ├── barcodes.tsv.gz
│    │     │     ├── features.tsv.gz
│    │     │     ├── matrix.mtx.gz
│    │     ├── filtered_feature_bc_matrix
│    │     │     ├── barcodes.tsv.gz
│    │     │     ├── features.tsv.gz
│    │     │     ├── matrix.mtx.gz
│    └── metrics_summary.csv

using raw_feature_bc_matrix or filtered_feature_bc_matrix as necessary for your data.