I have a custom GTF that is made up of experimentally determined exons and transcripts and includes the Ensembl gene ID for each entry. Some of these entries are known annotations and others are new. I would like to merge these with a gencode annotation GTF. My first thought was to do:
cat gencode.vM26.annotation.gtf custom.gtf > combined.gtf
and then sort the combined GTF, but this would result in redundant entries as the files contain some common annotations.
My next idea was to use stringtie with the gencode GTF as my reference:
stringtie --merge -G gencode.vM26.annotation.gtf wSmale.isoforms.gtf -m 0 -F 0 -T 0 -i -o test.gtf
but this forces a rename of the transcript prefix to "MSTRG" (by default) which results in a loss of information. (For my stringtie parameters, I wasn't sure how to choose them well so I just picked the the most permissive, is this problematic?). I would like to merge without renaming my custom file entries.
Does anyone have a solution to this problem?