I would like to align trimmed and filtered FASTQ files to the mm9 (mus musculus) reference genome to analyze 3'-UTR via STAR aligner.
My downstream applications did not work and I wonder whether I have used the right genome and the right annotation file.
I downloaded and used from ftp.ensembl.org/pub/release-67/fasta/mus_musculus/
Mus_musculus.GRCm38.dna_sm.primary_assembly.fa (DNA, FASTA)
would it be better to use cDNA?
Mus_musculus.NCBIM37.67.cdna.all.fa.gz. (cDNA, FASTA)?
Thanks for helping