Dear Biostar Community,
I would like to know if salmon uses phred scores while pseudoaligning (and/or validating mapping)?
- I checked Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417–419. doi:10.1038/nmeth.4197 and I did not find any reference to phred score;
- In the code, there is only one reference to phred and it does not seem to be used anywhere else.
In the negative, what is the reason behind this the choice?
Thanks in advance,