# MCScanAnchorsAdapter

Auto-generated config schema for the current JBrowse release — see the
[config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the
`comparative-adapters` plugin.
[View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/comparative-adapters/src/MCScanAnchorsAdapter/configSchema.ts).

## Example usage

```js
{
  type: 'SyntenyTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg19', 'hg38'],
  adapter: {
    type: 'MCScanAnchorsAdapter',
    uri: 'https://example.com/data.anchors',
    bed1: 'https://example.com/query.bed',
    bed2: 'https://example.com/target.bed',
    assemblyNames: ['hg19', 'hg38'],
  },
}
```

_See the **Config slots** section below for all available configuration fields._

:::caution Gotcha

The anchors file carries no coordinates: a gene is placed by matching its id
against column 4 of a BED, byte for byte. A row naming a gene neither BED has is
dropped, so a partial mismatch draws fewer ribbons than the file holds rather
than erroring, and only a file where no row resolves fails the track. Ids get
mangled by isoform suffixes, by BLAST truncating a FASTA header at the first
space, and by jcvi stripping suffixes unless run with `--no_strip_names`. BED
column 1 has to match the assembly's reference sequence names too, and a name
the assembly does not have draws nothing at all.

:::

used to load MCScan (jcvi) `.anchors` files with their two BED files

See the [MCScan anchors tutorial](https://jbrowse.org/jb2-staging/docs/tutorials/mcscan_synteny_grape_peach),
which also covers converting an MCScanX run into these files.

## Related links

- **Track:** [SyntenyTrack](../syntenytrack)
- **Display:** [DotplotDisplay](../dotplotdisplay)
- **Display:** [LGVSyntenyDisplay](../lgvsyntenydisplay)
- **Display:** [LinearSyntenyDisplay](../linearsyntenydisplay)
- **Display:** [MultiWaySyntenyDisplay](../multiwaysyntenydisplay)

## Config slots

These slots go inside the track's `adapter`:
`"adapter": { "type": "MCScanAnchorsAdapter", ... }`. It also accepts the
[shorthand](https://jbrowse.org/jb2-staging/docs/config_guides/file_types#the-uri-shorthand) keys `uri`,
`baseUri`, `bed1`, `bed2`, `chromSizes`, `csi`, `htsgetBase`, `nhUri` in place
of writing a location slot out. Slot types (`fileLocation`, `frozen`, ...) are
explained in the [config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types).
Slots a base configuration contributes are listed here too, so this table is the
whole surface.

<!-- prettier-ignore -->
| Slot | Description |
| --- | --- |
| <span id="slot-mcscananchorslocation">**mcscanAnchorsLocation**</span><br>[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = <code>{ uri: '/path/to/mcscan.anchors', locationType: 'UriLocation' }</code> | location of the `.anchors` file from `python -m jcvi.compara.catalog ortholog`: one line per anchor pair, naming a gene in each genome. The gene names are resolved to coordinates through the two BED files. |
| <span id="slot-bed1location">**bed1Location**</span><br>[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = <code>{ uri: '/path/to/file.bed', locationType: 'UriLocation' }</code> | BED giving coordinates for the gene names in the anchors file's first column, i.e. the query assembly's genes. Written by `python -m jcvi.formats.gff bed`. |
| <span id="slot-bed2location">**bed2Location**</span><br>[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = <code>{ uri: '/path/to/file.bed', locationType: 'UriLocation' }</code> | BED giving coordinates for the gene names in the anchors file's second column, i.e. the target assembly's genes. |
| <span id="slot-assemblynames">**assemblyNames**</span><br>`stringArray` = <code>[]</code> | `[query, target]` — the assembly `bed1Location` describes, then the one `bed2Location` describes. Getting the order backwards draws every link against the wrong genome rather than erroring. |