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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
name files more clearly
minor update
do not clobber results generated without using the merged GTF
when merging de novo results do not supply the known transcripts GTF file
Updated Transcript Assembly Merge (markdown)
Minor updates
use stringtie to merge transcripts for ref-guided and de-novo modes.
Update to cuffmerge to use vars.
Update FASTA path for assembly merge.
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