FiberHMM: chromatin footprint calling
FiberHMM calls chromatin footprints on single molecules from Fiber-seq (m6A,
Hia5) and DAF-seq (deamination, DddA and DddB) data, on PacBio and Oxford
Nanopore reads. For each read it finds nucleosomes, transcription-factor and
other sub-nucleosomal footprints, and the methylase-sensitive patches (MSPs)
between them. It writes every call, TF footprints included, as
Molecular-annotation
MA/AQ tags (nuc, msp and tf groups, with per-call quality bytes), and
keeps nucleosomes and MSPs in the fibertools ns/nl and as/al tags for
older tools. ft, FIRE and FiberBrowser read them.
Its emission probabilities are learned per sequence context, which corrects the large context bias of the marking enzymes and makes footprints the size of a transcription factor callable, not just nucleosomes. Across molecules, FiberHMM also finds recurrent footprint classes at a locus and measures how often each molecule carries them.
This chapter is a short overview:
To look at its footprints molecule by molecule, use FiberBrowser. FiberHMM and FiberBrowser are described in our bioRxiv preprint; see Cite.
The full documentation is at fiberseq.github.io/FiberHMM; the source is on GitHub.
FiberHMM 3.0 ships updated Nanopore Hia5 and DddB emission tables. Re-run calls made with earlier versions;
fiberhmm-check <your outputs>lists which files need it (upgrading from 2.x).