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update RegTools capitalization
fix URL examples for this years apache mount path
make alignment free its own module and updated TOC, footer, etc.
fixed formatting of navigation table that was missed earlier
fix missing script
fix remaining browser paths
add query for novel transcribed regions
rename files for IGV
add GTF filtering step
minor clean up and add todo item
fixing navigation bars at bottom of pages
fix navigation from Kallisto move
fix header for files coming out of R script
add brief regtools exercise
minor update
Updated Transcript Assembly Visualization (markdown)
Patch splicing visualization to account for no longer using Cufflinks