FluxSimulator produces paired-end reads that are effectively strand-specific, and for the purposes of testing quantifiers in the paired-end, unstranded case, I was simply running these tools without any strand-specification. But there may be some subtle effect due to the reads still being stranded, even if the tool doesn't know that, so it would be better to introduce a step in this case that randomises the strand of origin of the reads.
lweasel
commented
9 years ago
FluxSimulator produces paired-end reads that are effectively strand-specific, and for the purposes of testing quantifiers in the paired-end, unstranded case, I was simply running these tools without any strand-specification. But there may be some subtle effect due to the reads still being stranded, even if the tool doesn't know that, so it would be better to introduce a step in this case that randomises the strand of origin of the reads.