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.
- Convert SV files into a vg format; use MoMI-G tools or generate variation graphs on their own.
- Put annotation files you want to visualize on the
static/directory. - 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.