Hi,
I am using output files produced from rMATS 3.2.5. We used the pre-built STAR index and the included hg19 GTF file for annotation.
Unfortunately, the gene identifiers are "weird," in the sense that they are a mixed bag of Uniprot, NCBI, and UC identifiers. A large number of these are impossible to convert using any conversion methods I can find (secondary identifiers, or simply unable to find even with Google).
Has anyone else run into a similar problem, and how can I fix it? Since it is close to 1000 genes, it will be impossible to go line-by-line and identify each gene using chromosome position...
Thanks!