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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.
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
andaddnorm
) the same jar must be used (i.e. ifpre
was called from a 1.x jar,addnorm
must also be called from a1.x
jar). This is because 2.x jars only write the latestv9
of the.hic
file. - To upgrade your
v8
.hic
files tov9
, you can either rebuild files using themerged_nodups
or use the EMT Tool to build a newer.hic
file from an older one.
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.
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.