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.
It is important to make sure the chromosome identifiers are the same between your fasta reference and your gtf annotation. If one uses
chr1and the other just
1then you have a problem.
Thank you for that pointer - noted. Thankfully, if I understand correctly, Devon Ryan has pointed out that FeatureCounts is not impaired by this for UCSC and Ensembl chromosome names.