Who should I contact if I encounter a problem?

If you believe your problem may be encountered by other users, please post the question on biostars. Check to make sure your question has not been already answered by looking at posts with the tag deepDegron. Otherwise, create a new post with the deepDegron tag. We will be checking biostars for questions. You may also contact me directly at ctokheim AT ds DOT dfci DOT harvard DOT edu.

Can I run deepDegron using mutations annotated on hg19 and/or hg38?

Yes, deepDegron supports both hg19 and hg38. You will, however, need to download the relevant reference data for pyensembl first. We recommend ensembl release 75 for hg19:

$ pyensembl install --release 75 --species human  # download hg19 human reference data

For hg38, we recommend ensembl release 95:

$ pyensembl install --release 95 --species human  # download hg38 human reference data

To correctly specify which reference genome you are using, please supply the relevant ensembl release number to –ensembl-release flag in deepDegron.

$ deepdegron test [options] --ensembl-release 75 # for hg19
$ deepdegron test [options] --ensembl-release 95 # for hg38

Where can I obtain the training data for deepDegron?

You can obtain the set of mutations used for training from github for c-terminal degrons and n-terminal degrons.

What file format should I use for mutations?

deepDegron currently only reads MAF files. Please also see the File formats page.