This repository contains scripts that were used to make the captured_50x_morex_v2_ref.bed file.
The Morex reads were from the Mascher et al. 2013 The Plant Journal paper. The SRA BioProject number for the reads is: PRJEB1810. The SRA number for the reads is: ERP002487.
In this case, we are using Morex sample: ERR271706
Link to EMBL-EBI is: https://www.ebi.ac.uk/ena/data/view/ERR271706
Scripts used to make the captured_50x_partsRef.bed file for Morex v1 are located in the morex_v1 directory. Methods described below are for morex_v2.
Methods for each version of the reference genome are documented in README files in their respective subdirectories (i.e., morex_v1, morex_v2, and morex_v3).