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Result format? #15

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pna059 opened this issue Aug 27, 2022 · 3 comments
Open

Result format? #15

pna059 opened this issue Aug 27, 2022 · 3 comments

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@pna059
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pna059 commented Aug 27, 2022

Hi, I have run Armatus and got the TAD fragment-format results. I need to convert this to the bedpe and also find TAD boundaries.
I suppose that with 50 000 bp resolution, for example, the
1 1 5
1 6 8
translates to
chr1 0 50000 250000 300000
chr1 30000 35000 400000 450000
So what the TAD boundary would be? Should I consider not only directly neighboring TADS, but also those that are separated by one or more bins?
Not sure if I am doing it correctly - could you please navigate me?

Thank you
Pavla

@yihangs
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yihangs commented Aug 29, 2022

Hi Pavla,
Could you show me the output file of Armatus?

Thanks,
Yihang

@pna059
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pna059 commented Oct 11, 2022 via email

@yihangs
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yihangs commented Oct 25, 2022

Hi Pavla,
According to your description, I think in the example of
1 1 5
1 6 8

The first TAD is 0-249999, and the second TAD is 250000-399999. So the boundary of the first TAD is the bin (0,49999) and the bin (200000,249999); the boundary of the second TAD is the bin (250000,299999) and the bin (350000,399999)

Yihang

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