Hi all, I have run DESeq2 successfully in my RNAseq experiment and have observed some differentially expressed genes, so thats fine. There are 2300 genes in the annotated file, but only a handful of these are coming up as significantly DE (with adjusted p value). Many more are flagged as DE with the p value, but have an adjusted value above the sig threhold.
One question I have is regarding low counts. The samples were ran in paired end reads, so I have between 35-51million reads for the samples.. I know that DESeq2 accommodates the low/no read genes, but does it also take this into account for the stats; as in ignore them as though they were filtered out, or are they also considered as an additional sample comparison?
Could I (and indeed, should I) remove the zero counts from this analysis? And if there is scope to remove those with low counts, what would be a reasonable threshold to consider removing? For example, many samples have counts below 100, whereas some are in the tens or hundreds of thousands. At what point are the lower counts considered not necessary to include?