#Sample Mothur workflows
##MAKE SURE YOUR GLOBAL CONFIG IS SET TO ONLY UPDATE CURRENT BRANCHES DURING PUSHES
git config --global push.default=current
git init
git remote add origin master [email protected]:scholzmb/VantageMothur.git
git pull
git branch <branchname>
git checkout <branchname>mothur/ directory holds batch.m files for varying steps. run, in order
- mothur_batch_quality.m
- mothur_batch_shared.m
- mothur_batch_phylotypes.m
data/ contains sample sheets (also link.copy data here): stability.files (sample name\tread files) sampleTable.txt (sample name\tSampleType)
For alignment, you will need to symlink/copy Silva.v4. and silva.bacteria data/
run mothur batch files from data/