Which reference genome ?

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 genome to use from:

https://www.gencodegenes.org/human/

Genome sequence (GRCh38.p14) or Genome sequence, primary assembly (GRCh38)

& which one to use for GTF / GFF3 files?

Comprehensive gene annotation (ALL) or Comprehensive gene annotation (PRI).

Best,

Answer 1

[GenoMax]

If you are going to use aligners like STAR, HISAT2, bbmap : https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz

For programs that need transcriiptome files (salmon and kallisto): https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz

For GTF annotation: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.basic.annotation.gtf.gz