A intrinsic problem with Ensembl is that the annotation files provided does not match together (aka the different files (fasta, gtf do not contain information about the same transcripts) meaning the are not matched.
This problem is further described in this tweet (sorry for the unconventional way of providing the picture but was the easiest).
I have contacted the Ensembl people but they will not make any changes.
Would you consider updating the files in the pre-build indexes so all downloaded files match? This would make any downstream analysis requiring matching annotation easier.
A intrinsic problem with Ensembl is that the annotation files provided does not match together (aka the different files (fasta, gtf do not contain information about the same transcripts) meaning the are not matched.
This problem is further described in this tweet (sorry for the unconventional way of providing the picture but was the easiest).
I have contacted the Ensembl people but they will not make any changes.
Would you consider updating the files in the pre-build indexes so all downloaded files match? This would make any downstream analysis requiring matching annotation easier.
Cheers Kristoffer