I have a colleague who is recommend that we treat paired end data as single end data so that we get two technical replicates - it's an exploratory experiment, there's one replicate of 4 different cultivars of apple in two conditions.
Treating the PE data as SE seems ... wrong to me, but I can't immediately bring any objections to mind. Is there a reasonable reason that this should or shouldn't be done?
Cheers
Ben.
Treating the PE data as SE seems ... wrong to me, but I can't immediately bring any objections to mind. Is there a reasonable reason that this should or shouldn't be done?
Cheers
Ben.
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