Which reference genome, DNA or cDNA and why?

Question

[وفاء]

Dear Community,

The goal of my study is analyze Human RNA-seq and to take the gene count for RNA-seq and then apply the DESq2. I must use the most recent genome reference, but I am unsure of which FASTA file to use from Ensembl.

DNA or cDNA and why?

Best,

[dsull]

What tool are you using for your reads?

If you're using kallisto, salmon, or rsem, you use cDNA (coding DNA [aka transcriptome]) reference from ENSEMBL. It can be downloaded here: https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz