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`?
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-orientationand--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 outerand--report-position junction), or if it makes more sense to follow the defaults used byparse -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 read
and--report-orientation read`?Thanks again, Noura