Can hiccup not get the loop of 2K matrix?

Rosen Wen

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Jul 19, 2021, 9:03:37 AM7/19/21

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I try to use pre to generate 2K matrix (HIC file), and use hiccups to calculate the loops of the matrix, but the error is: exception in thread "main" Java.Lang.arrayindexoutofboundsexception: - 1, I try with test data, and the same result is obtained ~~~~~~~~~~ Is it necessary to use the resolution of "multiples of 5" to calculate "loops" with "hiccups"？

Rosen Wen

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Aug 13, 2021, 5:22:10 AM8/13/21

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Can someone help me（crying）

Muhammad Saad Shamim

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Aug 30, 2021, 1:07:37 PM8/30/21

to Rosen Wen, 3D Genomics

Hey Rosen,

Hope all is well. Sorry for the late reply.

How was this file generated? By default, 5kb, 10kb, and 25kb are used to find loops. If you want to call hiccups with custom resolutions, you will need to specify all the custom parameters as detailed here: https://github.com/aidenlab/juicer/wiki/HiCCUPS#detailed-example

Best,

- Muhammad Saad Shamim

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xian...@gmail.com

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Sep 8, 2023, 9:37:56 PM9/8/23

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Hi Muhammad,

Could you provide a recommended setting for 1kb resolution (-r 1000) using hiccups? Thanks a lot!

I used:

-k KR -r 1000 -f 0.1 -i 16 -d 2500 -p 22

The error message is:
Discarding invalid configuration: Config res: 1000 peak: 22 window: 16 fdr: 10% radius: 2500