Hi,

I am using DEseq2 to perform differential analysis of control and treated samples. However, I am not sure if DEseq takes into account number of initial reads in fastq files or number of aligned reads after salmon. Because I assume the greater the percentage of the reads are aligned, the greater the numReads is, does this get taken into account in DEseq2 or do I need to account for it myself before DEseq2?

Thank you,

Dan

The Salmon => tximport => DESeq2 pipeline takes into account the library size, robustly estimated using the median ratio of estimated counts across all genes. So the total number of reads in the FASTQ or total number of mapped reads are not used to calculate size factors in DESeq2.