Quantification with Salmon or STAR
Quantification converts cleaned reads into abundance or count data for differential expression.
Salmon
Section titled “Salmon”Salmon estimates transcript abundance efficiently from the preprocessed reads. It produces the abundance and count inputs consumed by downstream analysis.
STAR and featureCounts
Section titled “STAR and featureCounts”STAR aligns reads to the reference, then featureCounts summarizes aligned reads at the configured feature level. This option is useful when you need an alignment-based count workflow.
Interpret the metrics
Section titled “Interpret the metrics”Review mapping or assignment rates with organism, library preparation, read quality, and reference choice in mind. A low rate can indicate contamination, an incorrect reference, poor sample quality, or an assay mismatch. Keep the chosen method with any exported result.