Parse2 clarification

[NMaziak]

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Hello,

Thank you so much for creating such useful tools! I'm currently doing analysis on Micro-C data and had some questions on the parse2 options --report-orientation and --report-position.

Just for reference, we have paired-end reads (150 bp), so I thought it would be nice to try parse2. I'm just not sure if it would be more sensible to follow the defaults of parse2 (--report-orientation outer and --report-position junction), or if it makes more sense to follow the defaults used by parse -walks-policy all (--report-position outer). I would really appreciate it if I could understand better why the defaults vary between the two.

I have already tested both, and the maps looks very similar, as expected, but just wanted to gain some clarity and see if there are any caveats I am missing. For example, when is it sensible to use --report-position readand--report-orientation read`?

Thanks again, Noura