From 037dd8a0273d922319a70341303ddc3e766d1e6a Mon Sep 17 00:00:00 2001
From: Jonathan Robinson <jonrob@chalmers.se>
Date: Wed, 5 Aug 2020 16:18:05 +0200
Subject: [PATCH] doc: add readme for cellranger data subdirectory

---
 data/cellranger/README.md | 107 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100644 data/cellranger/README.md

diff --git a/data/cellranger/README.md b/data/cellranger/README.md
new file mode 100644
index 0000000..50a25d7
--- /dev/null
+++ b/data/cellranger/README.md
@@ -0,0 +1,107 @@
+# scRNA-seq Cellranger output files
+
+This directory should contain a folder for each sample (e.g., `lung0_2/`, `lung7_1`, `mln7_2`, consistent with the sample naming in the `metadata.csv` file in the parent `data/` directory), with each folder containing the following outputs from the cellranger pipeline: `barcodes.tsv`, `genes.tsv`, `matrix.mtx`.
+
+The directory contents should be organized as follows:
+
+```
+cellranger
+|-- README.md
+|-- lung0_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- lung14_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- lung14_3
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- lung28_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- lung28_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- lung28_3
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- lung7_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln14_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln14_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln14_3
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln28_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln28_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln28_3
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln7_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- mln7_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen0_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen0_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen14_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen14_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen14_3
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen28_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen28_2
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+|-- spleen7_1
+|   |-- barcodes.tsv
+|   |-- genes.tsv
+|   `-- matrix.mtx
+`-- spleen7_2
+    |-- barcodes.tsv
+    |-- genes.tsv
+    `-- matrix.mtx
+
+```