Hello, this is my first time working with Arabidopsis and I am quantifying with featureCounts as follows:
featureCounts -p --countReadPairs -t exon -g gene_id -a ../genome_arabidopsis/Arabidopsis_thaliana.TAIR10.57.gtf -o SRR14059988.txt ../alignment_hisat2/SRR14059988_sorted.bam
However, in my counts I am having counts associated with long non conding, ribosomals, mitochondrial and chloroplasts, is this normal?
ATMG01380, ATMG00150, etc.
I got the files from the ensembl: