README.md

Lep-MAP2 workflow

OLD.lep-MAP2 workflow for building genetic linkage maps

Documentation

1. Import data

mv file.loc to **02_data/*

2. Prepare data

00_scripts/utilities/joinMap_to_LepMap.sh 02_data/*.loc

3. Filtering module

sbatch 00_scripts/01_filtering.sh

4. Separate chromosome module validation

sbatch 00_scripts/02_separate_chromosomes_validation.sh

5. Evaluate LOD parameter

./00_scripts/utilities/count_nb_markers_lgs.sh

This step will format the output from the separate chromosome module to display the number of marker by LG. It is usefull to select a specific LOD and size limit tresholds

6. Separate chromosome module

first change the values for LOD and Size limit previously selected

sbatch 00_scripts/03_separate_chromosomes.sh

7. Join singles module

**first change the values for LOD and Size limit previously selected and the second LOD value **

sbatch 00_scripts/04_join_singles.sh

8. Order markers module

sbatch 00_scripts/05_order_markers.sh

The results will be in 03_output/order_markers.txt

lep-MAP2 repository

Lep-MAP2 repository

P. Rastas, F.C.F. Calboli, B. Guo, T. Shikano & J. Merilä (2015). Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example. doi: 10.1093/gbe/evv250

workflow in progress