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?