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Updated Installation (markdown)
add more questions and answers to the practical exercises
minor edit
minor update to install instructions
add regtools install instructions
merging install updates
update introduction.
Remove Cufflinks. Add StringTie and Ballgown. Update PATH.
Installation update: Remove TopHat2, Bowtie2, SAMStat and STAR. Update Picard to 2.6.0. Consistent fenced code blocks. Update $PATH.
minor update
revert flexbar install instructions
updated installation versions and added resources
added install instructions for hisat2