Hello, question regarding gene quantification for RNAseq: I've used HISAT2 to align my reads against the hg38 genome, and used UCSC annotation for this.
I now want to perform gene-level quantification using featureCounts. On the Ensembl website (ftp://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens), there are many options for GTFs:
Homo_sapiens.GRCh38.93.chr_patch_hapl_scaff.gtf.gz Homo_sapiens.GRCh38.93.gtf.gz Homo_sapiens.GRCh38.93.abinitio.gtf
What is the difference between these and which should I choose?
Also, the original alignment was done using UCSC gtf, would it be acceptable to then count using the Ensembl annotation? I want to switch because of this paper
Many thanks in avance for any help.