BRAKER3 to MCScanX

A collection of scripts to:

1. Transform BRAKER3 outputs into MCScanX format and compile data
2. Run the blastp search needed for MCScanX
3. Run MCScanX

Has been successfully run on both on Linux and macOS

Requirements

NCBI BLAST+, MCScanX (https://github.com/wyp1125/MCScanX)

R packages: tidyverse, Biostrings, plyranges, optparse

Scripts

BRAKER3-to-MCScanX.R Used to convert BRAKER3 gff and fastas into MCScanX approriate format. Requires BRAKER3 .aa, .codingseq and .gff3 along with a two letter prefix for the genome. The longest transcript of each gene will be used as its representative sequence.

BRAKER3-to-MCScanX.sh Takes BRAKER3 outputs, uses above Rscript to reformat for MCScanX, runs BLASTP searches, compiles data and runs MCScanX. As written it requires a tsv file species_list.tsv containing the species name in column 1 and desired 2 letter abbreviation in column 2; and BRAKER3 output to be in the directory data/braker/, with the file names corresponding to the species name in the species_list.tsv.