From 9ecd13ce76eb0e5ce83d64e3d6276631092054b5 Mon Sep 17 00:00:00 2001 From: Jonathan Robinson Date: Tue, 13 Oct 2020 16:47:45 +0200 Subject: [PATCH] fix: VDJ analysis README remove broken link to non-existent directory --- scripts/VDJ_analysis/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/VDJ_analysis/README.md b/scripts/VDJ_analysis/README.md index 2d30ab1..e896aa4 100644 --- a/scripts/VDJ_analysis/README.md +++ b/scripts/VDJ_analysis/README.md @@ -24,7 +24,7 @@ Note that there is a `metadata.csv` file in the [`data/`](../../data) directory | spleen14_3 | rna | v2 | M3 | infected | D14 | spleen | spleen14 | | ... | ... | ... | ... | ... | ... | ... | ... | -If a different dataset is to be used, this `metadata.csv` file will need to be updated accordingly. It is important that the **`dataset`** column is present and the entries match the names of the folders in the [`data/VDJ_OTUs/`](../../data/VDJ_OTUs) directory. Also, the **`mouse_nr`** column must be present in order to combine datasets based on subject (mouse) when performing the clone assignment. +If a different dataset is to be used, this `metadata.csv` file will need to be updated accordingly. It is important that the **`dataset`** column is present and the entries match the names of the folders in the `data/VDJ_OTUs/` directory containing the BCR sequencing data output. Also, the **`mouse_nr`** column must be present in order to combine datasets based on subject (mouse) when performing the clone assignment. The following sections describe each step of the VDJ workflow included in the `immcantation_VDJ_workflow.sh` bash script.