How to align reads to only one strand on a haploid reference genome?

Question

[izzy.yichao.cai]

Hi folks,

I have a set of ChIP-seq data from a haploid cell line. How do I map the reads to only one strand of my haploid genome since the reads can only come from one strand?

Thank you so much!

[Matteo Schiavinato]

Why would you want to do so with ChIP-seq data? As far as I know, you pull-down the DNA bound to a protein and you sequence it, so strand is not really a thing... if it was RNA, I would say it's valuable information, but with DNA, you're dealing with a double-stranded molecule!

[izzy.yichao.cai]

Jeez. I think I mistakenly think that haploid genome has only one strand of DNA. :p I ask a silly question.

Though it is haploid, the DNAs are still double-stranded (Just that it has only 23 chromosomes).

Thanks for pointing out!