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….
TLDR
| 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 |
Written on March 3, 2023