Eigenvector for higher resolution?

[Yunjiang Qiu]

Hi,

It seems that the eigenvector is only calculated for 500Kb or higher resolution. Is there a way to compute it for higher resolution? 

Thanks,

Yunjiang

[Neva Durand]

Hello,

It is now possible to do this offline with the Juicer tools; you can
then import the file into Juicebox as a 1D track. It's only done
offline because it can be an expensive computation at high resolution.

See this page of the wiki for more:
https://github.com/theaidenlab/juicer/wiki/Eigenvector

Best
Neva

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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab
www.aidenlab.org

[Yunjiang Qiu]

Cool, thanks! 

[Michael Johnston]

Hi Neva,

I just tried to run eigenvector (Juicer Tools Version 1.5.3) and the highest resolution I can run is 500kb. 

Beyond that, I simply get an empty file output.

Any suggestions? Thanks!

- Michael

Output below:

juicer_tools eigenvector KR ./aligned/inter_30.hic X BP 500000 ./aligned/eigenvector/eigen_X_500000bp.txt

Reading file: ./aligned/inter_30.hic

HiC file version: 8

juicer_tools eigenvector KR ./aligned/inter_30.hic X BP 100000 ./aligned/eigenvector/eigen_X_100000bp.txt

Reading file: ./aligned/inter_30.hic

HiC file version: 8

WARNING: Pearson's and eigenvector calculation at high resolution can take a long time

ls -lh aligned/eigenvector/

-rw-rw-r-- 1 michael.johnston1 michael.johnston1    0 Aug 18 11:35 eigen_X_100000bp.txt

-rw-rw-r-- 1 michael.johnston1 michael.johnston1 6.3K Aug 18 11:29 eigen_X_500000bp.txt

[Neva Durand]

Force with the -p flag. 

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[Aldo Tocci]

Hi Neva,

I'm trying to visualize my eigenvectors on Juicebox (version 1.8.8).

I have generated single chromosome eigenvectors with the following command:

my/path/to/juicer_tools_linux_0.8.jar eigenvector KR mysample.hic chr1 BP 50000 chr1_KR_50k_egen.txt -p

The output file contains just one column with values and when I try to load it as a 1D track, I get the following error

Do I need a particular format? 

Why isn't Juicer formatting the output file in the right way?

Thanks in advance

[Neva Durand]

The output is just a text file (similar to the other outputs from dump, which are also just text).  Convert it to the flavor of your choice to load in Juicebox or another track browser like IGV.  Wiggle is a good choice.

https://genome.ucsc.edu/goldenpath/help/wiggle.html

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[Aldo Tocci]

Thanks a lot!

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[Maoxuan Lin]

Hi Neva,

I am running juicer_tools eigenvector for some higher resolutions and it is taking pretty long time. Is there a way to speed up this calculation, multithreading for instance? I did not find a multithread parameter available for eigenvector calculation though and would like to confirm this. Probably it does not make sense at all to apply multithreading here...

Thanks,

Mao