Question: does salmon use "single-mapped" reads for quant? about salmon HOT 2 CLOSED

That's a surprisingly low mapping rate, maybe s/crappy transcriptome/very crappy transcriptome/ --- ;P. Anyway, yes, salmon counts single-end reads toward quantification. The way quasi-mapping works is that it first looks for paired-end reads that are mapped to the same contig. If those exist, it reports all such mappings. Otherwise, it reports the single-end mappings for each of the ends. The quantification is done in terms of "fragments", which is intentionally agnostic to the paired / single-end nature of the read mapping. If a paired end read maps, it counts as 1 fragment (though that mass of 1 gets proportionally assigned to the transcripts by the EM). If the pair doesn't map anywhere, then the single end mappings together all constitute 1 fragment (again, the same fragment whose mass gets proportionally assigned by the EM).

from salmon.

from salmon.