Low assignment rate with featureCounts

Low assignment rate with featureCounts

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I used STAR to align my reads (brain samples) to human reference genome. Getting good unique mapping rates (~70-90%).

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However, when I use featureCounts I get really low assignment rates.

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Here is an example command

featureCounts -p -t exon -g gene_id -s 2 -T 16 -a gencode.v38.annotation.gtf -o counts.txt Aligned.sortedByCoord.out.properPairs.bam

Any ideas why my assignment rate is so low? Should I be mapping to genes instead? Even if I do that I only get around 26% assignment which is better but still very low.


featureCounts


RNA-seq


STAR

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