Reference Database (-d)

For DeletionID, this is the "database" or directory with all the reference files used by identify-Deletion.sh. DeletionID provides reference files for yeast (sacCer3_Del) so you can quickly get started without building up the database from scratch. However, you are free to customize the database by adding a different set of coordinate new mappability scores or by looking at a different set of coordinate intervals.

Whether you use the provided pregenerated reference files or create your own, the database should use the following directory structure both to ensure that DeletionID can find the correct reference files.

/name/of/delDB
|--genomic_coord
   |--coord.bed
|--mappability
   |--mappability.tab

Below is a list of the files that DeletionID looks for during execution and some information on the provided yeast defaults.

• The coord.bed is the file with the genomic coordinate intervals we are looking for depletions within.
• The mappability.tab is the file with the calculated mappability scores for each coordinate interval within the coord.bed file. It is calculated using synthetic tiling and realignment using BWA. This will need to be regenerated if you use a different coord.bed file from the one provided.