Comparing SE and PE read samples

Hi! I have two batches of RNAseq data- one determined by/with paired-end reads and the other by/with single-end reads. I’m aware of the advantages and disadvantages of both approaches, but was wondering how appropriate it is to draw conclusions from a differential expression comparison (with DESeq2) between the batches.

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I guess the short and correct answer, if not the one you want to get, is:
It’s inappropriate without proper experimental design. If you have mixed SE/PE data for the same samples you could treat the sequencing technique as an additional factor in your experiment and, essentially, correct for its influence, but if sequencing technique and sample type are tied together, there is no way to disentangle them, and any conclusion you try to draw as to how much SE vs PE influences observed differences between batches is just speculation.


Right, that’s what I thought. Thanks!