Custom Input

This is an instruction for using custom input on MoMI-G. When you want to employ custom dataset, you have to do following procedure; see references.

  1. Convert SV files into a vg format; use MoMI-G tools or generate variation graphs on their own.
  2. Put annotation files you want to visualize on the static/ directory.
  3. Modify configuration file written in YAML.

MoMI-G data files

The list of formats that are accepted by MoMI-G is following. You should put them on the static/ directory and specify the file name on the YAML configuration file.

File type Extension Description Softwares
A succinct index of variation graphs .xg Variation graphs displayed in MoMI-G. (required) vg
Graphical alignment/map .gam Read alignment. vg
Comma-separated values .csv(.pcf) SV list for chromosome-scale view. MoMI-G tools
Browser extensible data .bed Used for converting gene names to genomic intervals.  
Compressed binary indexed BED .bb Annotation tracks. bedToBigBed
Compressed binary indexed wiggle .bw Annotation tracks. bedGraphToBigWig

If you want to use bed/gff/gtf files for custom tracks on SequenceTubeMap, you have to manually convert them into bigbed format.