'Can I use HISAT2 for alignment when doing the Chip-seq?
When I was doing the RNA-seq, I use the HISAT2 to do the alignment. However, during the chip-seq analysis, bowtie2 is widely used to do the alignment. But there is a parameter for HISAT2 to do the DNA-seq like analysis, --no-spliced-alignment. So, why not use HISAT2 during the Chip-seq analysis? Thank you!!
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