MAJIQ requires as an input an annotation of the transcriptome and currently only supports the GFF3 format as specified. The GFF3 annotation files used in the MAJIQ paper for mouse and human can be downloaded here, Mouse (Ensembl, mm10 build), Human (Ensembl, hg19 build)
If you would like to use a different annotation file you can use the following tool to convert a GTF file (e.g. downloaded from Ensembl) to the GFF3 format that MAJIQ accepts.
It is important to note that MAJIQ makes some assumptions when parsing the hierarchical GFF3 file and has some specific requirements: