What aligners to choose between Hisat2 and BWA for chip-SEQ analysis

Question

[Molinia]

Hello everyone,

I have a little question about the aligners, I just wanted to know, in order to make an analysis on transcription factor with Chip-SEQ experience, what aligner is best between BWA and Hisat2 and why ?? Can't decide which one to chose because I've seen some people who appreciate more hisat2 than BWA etc.... Thanks in advance :)

Answer 1

[ATpoint]

No preference. Both are accepted and appropriate with a large user base, and both will serve you well. Choose the one you feel more comfortable with. Aligners are a bit like choice of religion (I know, not a scientific statement) but for the end user this is what it is. It would surprise me if most users gave you an elaborate explanation why they use a certain aligner other than they are comfortable with it or someone suggested that tool when they were still beginners. Be sure to have samples with reasonable read length like > 50bp, if less you might consider bowtie as it is designed for very short reads.

[Molinia]

thanks for the reply. Just to ask, is there any advantages to use Hisat2 instead of BWA ? I mean, I've seen that if I choose BWA, I have to explain why this aligner and not Hisat2? You see what I mean ?

[i.sudbery]

Used with a standard genome index (like I think most people do), there is no advantage to HiSat2 over BWA for ChIP-seq. You'll probably find that BWA is faster.

However, it is possible to build Hisat2 indicies to be aware of variant positions in the genome and so map reads even if they contain these SNPs. However, I don't think this is particularly important for ChIP-seq applications unless you are trying to do allele specific ChIP.