Custom reference data

The pipeline uses reference data at various stages. If you're using a common genome assembly, these resources are pre-built and can be easily downloaded using refgenie pull, as described in the setup instructions. If the resources are not available, you'll have to build them. Read how to build refgenie assets in the refgenie docs. You may also learn about the current buildable assets to which refgenie knows the recipe.

Use a custom feat_annotation asset

The pipeline will calculate the fraction of reads in genomic features using the refgenie feat_annotation asset, but you can also specify this file yourself at the command line (--anno-name).

This annotation file is really just a modified BED file, with the chromosomal coordinates and type of feature included. For example, the hg38/feat_annotation asset looks like so:

chr1  70008   71585   3' UTR  . +
chr1  450702  450739  3' UTR  . -
chr1  685678  685715  3' UTR  . -
chr1  942695  943058  3' UTR  . +
chr1  942855  943058  3' UTR  . +
chr1  943252  943377  3' UTR  . +
chr1  943697  943808  3' UTR  . +
chr1  943907  944581  3' UTR  . +
chr1  944153  944574  3' UTR  . +
chr1  944202  944693  3' UTR  . -

Just like a standard BED file, the first three fields are:
1. chrom - the name of the chromosome
2. chromStart - the starting position of the feature
3. chromEnd - the ending position of the feature

Column four is the name column, in our case the name of our feature of interest. The fifth column is the score, which would determine how darkly an item would be displayed in a genome browser if you chose to set that or if the information in your file of interest has ascribed a score to the features. The final, sixth, column is the strand column.

After creating your BED file, you can point the pipeline to it using the --anno-name option followed with the path to your file. The pipeline will then use that file to determine the fractions of reads that cover those features. You could also tag this as an alternative refgenie managed asset.