salmon quant -t ${REF} --fldMean 200 --fldSD 20 --numBootstraps 40 -l U -a ${BAM}.sorted.bam -o ${BAM}_U
salmon quant -t ${REF} --fldMean 200 --fldSD 20 --numBootstraps 40 -l A -a ${BAM}.sorted.bam -o ${BAM}_A
Thank you very much.
Hien
It's likely the reason you're seeing the behavior you are is because of the way that Salmon's library type is handled as part of the underlying probabilistic model. Specifically, under the default parameters, the library type specifies that alignments that are compatible with the library type should be given a much higher a prior probability than those that are incompatible with it. However, if the only alignments for the fragments are incompatible alignments, they will still be used. If you want Salmon to strictly ignore incompatible fragments, you should pass the parameter `--incompatPrior 0` to Salmon. This will cause incompatible alignments to be given a 0 probability, and hence discarded. Please let me know if this provides the behavior you were expecting.
Best,
Rob