mapped reads (m aligned) is higher for a subset sample?

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Hi Biostars Community,

These are from patient rheumatoid arthritis samples.

My % aligned was at about 85% for all samples, and mapped reads (M aligned) roughly about 6-9 (million) for most of the samples. However one of the samples and all of its technical replicates had mapped reads in the 16-18 (million) range. This was also similiar before mapping to the transcriptome using salmon. What could be an explanation for this?

This picture is before mapping.

enter image description here


This picture is after mapping:

enter image description here

Thank you in advance. I will pay it forward!


salmon


fastqc


multiqc


RNA-seq

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