Image processing isolates loop, but some of them not called.

PouletAxel / SIP

SIP: Significant Interaction Peak caller

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Image processing isolates loop, but some of them not called. #14

Closed gdolsten closed 1 year ago

gdolsten commented 3 years ago

Hey, here is an image of how a Hi-C matrix looks post-image-processing: (I removed the diagonal for visualization purposes).

It calls most of the loops, but it misses the prominent loop in the top-left...Do you know why this loop is not being called? It seems quite prominent so I was wondering which parameters could be changed to find it. Is it just too large for the loop-calling program?

These loops were called with the following parameters: -res 1000 -d 10 -fdr .1 -del false -nbZero 10 -mat 500 -t 1000

PouletAxel commented 3 years ago

Hi, Can you send us the command line please?

On Fri, 19 Feb 2021 at 15:29, gabedolpten notifications@github.com wrote:

Hey, here is an image of how a Hi-C matrix looks post-image-processing: (I removed the diagonal for visualization purposes).

[image: image] https://user-images.githubusercontent.com/78431504/108557653-e706b680-72c6-11eb-9834-0105cac990da.png

It calls most of the loops, but it misses the prominent loop in the top-left...Do you know why this loop is not being called? It seems quite prominent so I was wondering which parameters could be changed to find it. Is it just too large for the loop-calling program?

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gdolsten commented 3 years ago

The parameters were as follows: -res 1000 -d 10 -fdr .1 -del false -nbZero 10 -mat 500 -t 1000

PouletAxel commented 3 years ago

Can you send me the .tif corresponding to this image please?

On Fri, 19 Feb 2021 at 18:54, gabedolpten notifications@github.com wrote:

The parameters were as follows: -res 1000 -d 10 -fdr .1 -del false -nbZero 10 -mat 500 -t 1000

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gdolsten commented 3 years ago

Do you want the one that is _N, that is _processed, or the one without any of these?

PouletAxel commented 3 years ago

You can send me the three of them via my email (pouletaxel@gmail.com)

On Sun, 21 Feb 2021 at 00:30, gabedolpten notifications@github.com wrote:

Do you want the one that is _N, that is _processed, or the one without any of these?

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