This tool imports a collection of genomic region datasets, and associates to each region multiple genomic feature measurements. It allows to align the regions in multiple ways (center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the measurements) and to create a graphical representation of the feature measurements in each region datasets (aligned curves or pointwise quantile curves).
Region datasets
Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr start end (extra columns present in the input file are ignored). Regions can be of different length:
chr2 49960150 50060150 chr2 55912445 56012445 ...
Feature measurements
Feature measurements corresponding to all the regions can be provided as a BED or Tabular file with tab delimited columns chr start end value:
chr2 49960150 49962150 0.9426 chr2 49962150 49964150 0.7816 ...
Each feature must be measured in windows of a fixed size inside all the regions (missing values must be indicated as NA). Another way to import feature measurements is from a Tabular file with the first three columns chr start end corresponding to the different genomic regions, followed on the same row by all the measurements in fixed-size windows:
chr2 49960150 50060150 0.9426 0.7816 0.8921 ... ... 1.2063 chr2 55912445 56012445 0.8719 0.9975 1.1619 ... ... 0.9601 ...
Output
The tool returns:
1-3 can be used as input of the tool IWTomics Test and Plot
Notes
This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy - fabio.cumbo@iasi.cnr.it) and Marzia A. Cremona (The Pennsylvania State University, USA - mac78@psu.edu).
It implements a simplified version of the methods smooth and plot for IWTomicsData objects. The complete version can be found in the R/Bioconductor package IWTomics (see vignette).
Example data can be found at: