Question: HISAT2 or SALMON AND KALLISTO
0
gravatar for biks.kestro
3.3 years ago by
biks.kestro10
biks.kestro10 wrote:

What is good for RNASeq analysis, HISAT2 or Salmon and kallisto ? Please advise if other good option is available.

rna-seq • 1.6k views
ADD COMMENTlink modified 3 months ago by ATpoint36k • written 3.3 years ago by biks.kestro10

In my sub-field (environmental eukaryotes), Salmon is more popular than the other two, but as others have mentioned below all three are established and respected methods. Salmon and kallisto are extremely similar. I do not have experience with HISAT2.

ADD REPLYlink written 3 months ago by N15120
5
gravatar for genomax
3.3 years ago by
genomax87k
United States
genomax87k wrote:

Have you looked at the respective publications/web pages to understand the differences? Since we don't know what your intended application is the answer would be "depends on your needs".

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by genomax87k
1

Adding on this, all methods are accepted and well-tested. Each has their individual strengths and weaknesses. Please read benchmarking papers for details.

ADD REPLYlink written 3 months ago by ATpoint36k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 842 users visited in the last hour