human genome files

human genome files

0

Hi all,

Just wonder to know about these two questions?
what is the main difference between the two genome files (Homo_sapiens.GRCh38.dna.primary_assembly.fa and Homo_sapiens.GRCh38.dna.fa) located in the ensemble database?
which one should I use for whole-exome sequence alignment?

I used Homo_sapiens.GRCh38.dna.fa for the alignment, and later on, when I did future count using featureCounts function as below, the whole matrix was zero. Just wondering in case Homo_sapiens.GRCh38.dna.fa was the wrong file for my alignment.

featureCounts -t exon -g gene_id -a Homo_sapiens.GRCh38.105.gtf -o Ensembl_counts_gtf.txt *.bam 

Best,
amare


alignment


featureCounts

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