Annotation files

Annotation files contain all the information on genes and transcripts spada needs to work, from gene coordinates to isoform features and protein-protein interactions. We have pre-generated annotation files for some of the common annotations below. To use one, download it to your working directory, and add the corresponding flag in spada.

• GENCODE v23, --annotation gencode_v23.pklz.

All the annotation files were generated on GRCh38 and BioGRID version 153. Disordered regions were calculated using IUPRED and Pfam and ProSite features were retrieved from ENSEMBL.

Creating your own annotation files

If the annotation file you need is not available above, you can generate them yourself via spada init. We provide a script at annotation_files/get_gencode_annotation.nf that vastly simplifies the process if using GENCODE/ENSEMBL annotation.