STAR: Is it ok to align with an index created from genecode but count features from gtf from ensembl?

Question

[simplitia]

I'm wondering if there maybe some coordinate issues as with UCSC and ensembl. I happen to have bam files which were aligned with STAR using indices that were created from gencode however, I would like to use htseq count but with gtf donwloaded from ensembl instead?

thanks! A

[ATpoint]

Why not keeping things simple and download GTF from Gencode? There are a lot of pitfalls in bioinformatics due to different formatting of files and gene names etc. Don't mix annotation files!

Answer 1

[Kristoffer Vitting-Seerup]

You will most likely have a problem. Gencode uses chromosome names: "chr 1", "chr 2" etc. Ensembl uses chromosome names "1", "2" etc. Why not use gencode gtf file?