Frequently Asked Questions

Why is chess sim so slow?

A common cause for long runtimes of chess sim is when the input files are in Cooler format. chess sim compares observed/expected transformed matrices, and these are often not precomputed and stored in this format. If your runs spend a long time in the “INFO Loading query contact data” step, consider converting your data to Juicer, or FANC format, as these usually store observed/expected values (see here).

Why do I get “ERROR No valid region pairs found” when using Juicer .hic files?

Juicer removes the “chr” prefix from chromosome names. This can cause chromosome names in Juicer .hic files to not match chromosome names in pairs BEDPE files created with chess pairs. Please check whether the chromosome names in your pairs file match those in your .hic file.

Can I use CHESS to compare the results of loop calling software between samples?

Some users have asked whether it’s possible to use CHESS to compare loop calls between samples, by supplying the BEDPE file output by a loop calling tool as the input pairs file for CHESS. This not recommended, for reasons explained below.

BEDPE files used to specify loops typically specify a small (< 10x10 bins) region that is located away from the diagonal of the matrix. In contrast, the BEDPE files produced by chess pairs and used as input to chess sim specify large (e.g., 100x100 bins) regions that are located at the diagonal of the matrix.

While it may be possible to use CHESS to examine off-diagonal regions, this is so far untested and may not work as expected! Instead, we recommend creating on-diagonal windows that span the width of the whole loop, or using chess pairs to create windows that tile the genome and run a genome-wide comparison between your samples.