.........................Error: the chromosome combination 1_10 appears in multiple blocks

[Robin van der Weide]

When I use juicebox_tools pre without the -d option, I get the error message that a chromosome combination appears in multiple blocks. What does this actually mean? And how can I fix this?

[Neva Durand]

Hi Robin,

The input file should have all chromosome sub matrices  (1-1, 2-2, ... as well as interchromosomal 1-2, 1-3, ...) together in the same place in the file. We only store the currently processing sub matrix; otherwise the memory requirements would be prohibitive. This also means that for interchromosomal reads, you might need to reorder and sort, so that the read end with the lower chromosome is always the first read. 

This should be documented (note to our developers). 

On Tuesday, March 15, 2016, Robin van der Weide <robin...@gmail.com> wrote:

When I use juicebox_tools pre without the -d option, I get the error message that a chromosome combination appears in multiple blocks. What does this actually mean? And how can I fix this?

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org