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+## GRAVI data folder
+
+This folder is the common recommendation for placing all data files.
+The recommended structure is:
+
+- Place alignments in a directory called `bam` or `aligned`. This can be customised in `config.yml`
+- Place any external data in a directory call `external`. This is where the GTF, blacklist or any other files should be placed. Again, these paths can be customised using `config.yml`