Annotation GTF/GFF Arabidopsis thaliana

Question

[san96]

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:

Arabidopsis_thaliana.TAIR10.57.gtf Arabidopsis_thaliana.TAIR10.dna.toplevel.fa

[san96]

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