FAQs

Feel free to suggest questions to add to this list by emailing us at aidenlab at bcm dot edu.
Also check out the public forum.

Version issues (1.x vs 2.x)

Juicer and Juicer Tools are under active development, and we have not made official releases for version 2 yet. In general, while we try to maintain backward compatibility, it is not always possible. Some general guidelines:

• Files built with Juicer Tools 1.x should be readable by all future 2.x jars for most tools (HiCCUPS, Arrowhead, etc).
• For file writing tools (pre and addnorm) the same jar must be used (i.e. if pre was called from a 1.x jar, addnorm must also be called from a 1.x jar). This is because 2.x jars only write the latest v9 of the .hic file.
• To upgrade your v8 .hic files to v9, you can either rebuild files using the merged_nodups or use the EMT Tool to build a newer .hic file from an older one.

KR is not available for a particular chromosome/region

The KR algorithm sometimes does not converge for a particular region/chromosome. When the normalization fails for a chromosome at a specific resolution, the .hic file does not contain the normalization vector for that resolution as well as higher resolutions. More recently, we have added a new normalization method, called SCALE to remedy this. You can use addNorm in newer versions of juicer tools to use SCALE instead of KR.

Normalization failing for fragment (FRAG) resolutions or FRAG resolution questions in general

We've actually moved away from fragment resolution maps. Unless you are doing some very specific/specialized development, you probably don't need them. Going forward, Juicer 2 will no longer build fragment resolutions. Instead, you can build higher basepair (BP) resolution maps. Remove the -f flag for pre or add the -F flag for addnorm to ignore these FRAG resolutions.