What shoud i do if multiQC stats from featurecounts show that only 3% of my aligned reads is assigned even 70% of my reads are aligned in STAR?

05 January 2024 1 6K Report

During my RNAseq data analysis, I encountered a problem where the statistics from MultiQC from the STAR method showed that 70% of my trimmed reads were aligned, but when I ran using the same BAM files, it said that only 3% of my reads were assigned.

Why is that? Should I proceed further or do I need to perform additional checkups? For reference i used HG38.p14 version from NCBI.

Markus Glaß

Hi Pratanu,

have you checked if the parameters of featureCounts were set properly (correct annotation used, strand orientation, etc.)?

I would have a look at the bam files using a genome viewer, like IGV and check if there are reads at certain genes that I would expect to get reads for sure.

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