1.1 Programs available in Nucleo-Miner Package
The Nucleo-Miner package has been designed to integrate a large variety of information required to finely map and characterize nucleosome occupancy and modifications
at a genome-wide scale. To do so, Nucleo-Miner package contains
a series of programs in order to efficiently store the data, to perform
the analyses and to import/export data/results in various formats.
Follows a list of the different command line
programs included in the Nucleo-Miner package.
- NMmpa - Format Mummer output for tiling probes mapped on genome sequence.
- NMcl2tab - Extract and merge tiling array data
- NMmprb - Extract only the probes that share the same genomic and array coordinates between a reference and a query
- NMtdb - Create a tilling array database
- NMt2feat - Integrate tilling array values within custom annotations
- NMt2featcis - Look at the tilling array profile around custom annotations
- NMhmmfit - Fit a HMM to indentify nucleosomes
- NMhmmvit - Apply the Viterbi algorithm to call nucleosomes
- NMalign - Align nucleosome occupancy profiles between two genomes
- NManova - Fit an ANOVA nucleosome by nucleosome to detect SNEP
- NManout - Output results obtained with NManova
- NManowin - Summarizes results obtained with NManova using bin or sliding windows along the genome
- NManofoc - Summarizes results obtained with NManova by computing overlap score with custom annotations
- NMt2feat2 - Fast integration of tilling array values within custom annotations
- NMalign2 - Fast align nucleosome occupancy profiles between two genomes
- NManova2 - Fast fit an ANOVA nucleosome by nucleosome to detect SNEP
- NManout2 - Output results obtained with NManova2
- NManofoc2 - Summarizes results obtained with NManova2 by computing overlap score with custom annotations
- NManowin2 - Summarizes results obtained with NManova2 using bin or sliding windows along the genome
The use of these programs is described in this manual. Each chapter
provides detailed definitions of the programs, followed by example.