Kallisto v HiSat
In attempting to get quick comparison of alignment across genome, the question arises what is the difference (and accuracy) of kallisto (psuedo-align) and hisat. Spoiler - I was quite surprised with hisat w and w/o gtf. This is A pulcra RNA-seq data….
|Genome||kallisto||HiSat||HiSat no splice||Col5||Col6|
|Amil_v2.1||“p_pseudoaligned”: 84.9, “p_unique”: 82.2||76.02% overall alignment rate||76.00% overall alignment rate|
|Adig_1.1||“p_pseudoaligned”: 72.8,”p_unique”: 69.8||57.46% overall alignment rate||57.40% overall alignment rate|
|Ahyacinthus.chrsV1||“p_pseudoaligned”: 82.1,”p_unique”: 80.4||68.10% overall alignment rate|