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fix tables for real this time
Revert "fix the navigation tables on wiki pages" This reverts commit 1c78d5acac208efcaf4c284160febd715b2ddcb0.
fix the navigation tables on wiki pages
fix strand parameter name
fix exercise numbering
Updated Alignment (markdown)
add more questions and answers to the practical exercises
minor update
Add align var to env.
update command line param description.
Update index var. Drop Cufflinks option.
Update alignment to use ENV variable for reference index.
use full path to picard JAR
Update the alignment reference index path and the path to FASTA that is indexed.
Switch to HISAT2 only and reduce complexity of commands. Combine sort/view with new multi-threaded samtools.
added HISAT2 alignment and indexing sections