Zea mays Germinate -- Makefile to Generate Some Maize Genomics Resources

zmays_germinate is reproducible genomic resource generation for Zea mays. Information comes from Ensembl (but maybe later, from MaizeGDB).

Versions

There are three major releases of the maize genome: AGPv1 (from Schnable et al., 2009), AGPv2, and AGPv3. Ensembl supports AGPv2 and AGPv3, but their release cycle and version numbers are based on their Ensembl genome scheme.

The Makefile contains a variable AGP_VER that can be changed to either: AGPv2.17 (the last Ensembl release of AGPv2) or AGPv3.20 (the most recent release of AGPv3). Note that this only changes what the makefile gathers -- transcript databases created by R/txdb.R will use Ensembl's mart databases, but will explicitly version everything created under the directory data.

Data

All data is downloaded to data/, in directory corresponding to the AGP version.

Sequences

A Makefile downloads all non-masked sequence from chromosomes 1-10, and Pt and Mt. Currently, the "unknown" chromosome is ignored (but this and other changes can be easily made to the Makefile). Sequences are unzipped and combined into a file with the suffix _combined.fa in the particular version directory.

Annotation

Ensembl's AGPv2 version only contains a GTF file, but a GTF file and GFF3 file are available for AGPv3.

Running

To adjust the AGP version, uncomment the appropriate AGP_VER. Then, run:

$ make all

If you're using AGPv3, which has a GFF3, you also run make gff.