Choice of read length
SE
We assessed the impact of differing read length on our ability to detect DEGs by truncating reads to mimic common Illumina sequencing configurations (100 nt SE, 75 nt SE, and 50 nt SE), and compared DEGs recovered to those found using 151 nt. Overall, for the strongest biological signal observed at Days 2-14, we found very little impact, the overlap in DEGs was >90% for all configurations, and it was 95% and 94% for the 100 nt and 75 nt simulations, respectively, based on Jaccard index. Our findings are largely in agreement with prior work examining this relationship: Chhangawala et al. (