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make alignment free its own module and updated TOC, footer, etc.
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
use the merged GTF to generate new estimates, but not the annotated and merged GTF where some transcripts are lost
do not clobber results generated without using the merged GTF
Updated Differential Splicing (markdown)
Minor updates
Add comment to see DE section for running ballgown
Add ref-guided and de-novo DE, not really differential splicing.
Use vars for Diff-splice.
Update DE modes and Alternative Expression to use HISAT2 BAMs and simplified paths.
fix all links to cufflink manual pages
add flowchart
Remove redundant header syntax
Initial revision for Module2, Module3 and Module4