Hisat2 or Bowtie2 for ChIP-Seq Data?

Question

[hkarakurt]

Hello everyone, I am analyzing a ChIP-Seq data and I aligned them with Bowtie2 with default parameters. I used to use Hisat2 for my RNA-Seq data but I heard Bowtie2 gives better results with short reads. Actually a friend said that

I have done the alignment step but I need to be sure.

Is Bowtie2 better than Hisat2 with ChIP-Seq data? Do default parameters give bad results?

Thank you.

Answer 1

[EagleEye]

• HISAT2/STAR/Tophat: suitable for transcriptome based or RNA-seq alignment (splice-aware aligner)

• Bowtie/Bowtie2/bwa: suitable for genome based alignment (ChIP-seq/WGS)

[mollitz]

"HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)."

• HISAT2 website (https://ccb.jhu.edu/software/hisat2/index.shtml)