Hi,
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)
Mus_musculus.NCBIM37.67.gtf

would it be better to use cDNA?
Mus_musculus.NCBIM37.67.cdna.all.fa.gz. (cDNA, FASTA)?

Thanks for helping



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