# MGC Tracks

Information about the status of MGC clones are downloaded from NCBI and used in constructing a MGC-specific tracks. A track of MGC full-CDS clones is built for all browsers, while tracks containing the status of other MGC clones is constructed for the MGC browser.

## MGC Pipeline Data

A dumps of tables from the MGC track database are deposted every Wednesday at 2 am EST at `ftp-private.ncbi.nih.gov`. The data is then processed by `mgcImport` to create tab files used to load the `mgcStatus` table. A script `mgcDownload` is run by cron to download and process the data.

### Directory structure

- `$gbRoot/data/mgc/$date/` - Directory containing MGC data for download done on `$date`:
  - `library.gz` - MGC library table dump.
  - `clone.gz` - MGC clone table dump.
  - `fullength.gz` - MGC fullength table dump.
  - `stage1.gz` - MGC stage1 table dump.
  - `table.descriptions` - schema for mgc tables.
- `$gbRoot/processed/mgc/$date/` - Directory containing MGC data generated from corresponding download directory.
  - `mgcStatus.tab,gz` - Tab file containing summerized status information for all MGC clones, created locally by `mgcImport`.
  - `mgcFullStatus.tab.gz` - Subset of `mgcStatus.tab,gz` for the MGC full-CDS clones. This is used to load browsers that will only have the full-CDS track. It is signficantly smaller than the full table.

## MGC Alignment Tables

## MGC-status table

MGC tables for verified full-length clones are created for use on all browsers, while the MGC-specific browser contains additional tables indicating the state of clones in the MGC pipeline.

- `mgcFullStatus` - Table containing status information about full-CDS MGC clones.
- `mgcStatus` - Table containing status information about all MGC clones.
- `mgcFullMrna` - PSL table of MGC full-length mRNAs.
- `mgcGenes` - MGC full-length mRNAs with CDS annotation.
- `mgcIncompleteMrna` - PSL table of MGC mRNAs which are not full length or contain other errors.
- `mgcPickedEst` - MGC ESTs that have been picked for sequences or are in the sequencing pipeline.
- `mgcFailedEst` - MGC ESTs where sequencing failed.
- `mgcUnpickedEst` - ESTs from MGC libraries that have not yet been picked for sequencing.