When performing differential expression analysis, should genes with low read counts be removed before or after normalization?
The more genes you have the more robust the scaling factor is (among the reason why one doesn't normalize to ERCC spike-ins without a compelling reason), so I suppose in theory it's better to filter after determining the scale factor. Having said that, I'd be surprised if the results changed much either way. Unless you end up filtering out a LOT of genes the scaling factors should be fairly robust to the change.