changed the scan.sh a bit
Tested through all eight steps
Correction to mrnaseq/0-download-and-save.txt
merged to master updates
Update documents
Merge pull request #67 from LSheneman/origin/literate

Merging up so we can ll clean it up
Update 1-quality.txt
Update 0-download-and-save.txt
fixed merge conflicts in 1-quality
Merge pull request #68 from ged-lab/Literate-Leigh

Literate leigh