Forked Aphaneogaster transcriptome assembly repository from /projects/climate-cascade/projects/ApTranscriptome

New assembly uses an .Rmd script with `system()` calls to run programs such as `flash` and `Trinity`

This has the *major* advantage that I can use a single script, developing each stage as I go
along, and caching the results so I don't have to re-run each individual program which can take
many hours.

Also makes it easier to intergrate R stats in single script.
First test of complete script for assembly

  --> Trim_galore for QC (WORKS)
  --> FLASH to merge overlapping reads (WORKS)
  --> diginorm for digital normalization
  --> Trinity for transcriptome assembly

Added supplemental python scripts needed for processing...
Updates to assembly script - debugging digital normalization
Added README
Added script to compare Trinity assemblies
Added code to evaluate assembly by BLASTing spike-in sequence
Update to assembly script

  - assembly each colony (Ar, A22) independently
  - requires performing diginorm independently for each

Motivation was to deal with issue that combined assembly resulted in
separate transcripts of orthologs for each colony. Decided best to
assemble separately and then search for orthologs between assemblies.
Debug script to correctly  files
Functioning script through transcriptome assembly with merged and normalized reads!

Caught error message in Trinity output - the 'extendedFrag' reads lacked Illumina tags "\1"
and were ignored in assembly. Added tags using `add-illumina-tags.py` script and fixed.
Cleanup directory
Updated script to evaluate assembly based on in silico spike-in reads. Added function 'assembly.spikein.eval' to assemble_functions.R to do this. Started to add uclust and CAP3 transcriptome filtering to assembly script.
Continuing work on assembly script

  Bugs fixed
  - mistake to remove `trimclip` reads - need these for expression quantification!!!

  Additions
  - merge chimeric and redundant transcript using CAP3
  - remove *in silico* contigs from A22 assembly
  - gene expression quantification using `sailfish`
Updated script through expression quantification
Updates to script
Added new fucntion `rename.trinity.transcripts` to `assemble_functions.R`.
Use this function to rename assembly transcripts to more useful names.

Some cleaning-up of script.
Updates to script. Changed transcript naming convention to 'ApVT_000000.1' where the dot(.) delinates alternative transcripts of the same component. Working on adding BLAST annotation. Due to computational nature (e.g. many DAYS) will simply describe how this is done but not include as R chunk
New script *ApTranscriptome_TR.R* that documents current version of analysis using full Trinity assembly from VGN. Command-line programs are described instead of run in script, and only R code is dynamically-generated.
Updated script through identifying responsive genes. Implementing qvalue
Update README
Added function RxNseq that performs analysis, including FDR, to detect responsive genes. Output is a dataframe with pvalues, qvalues for each transcript, and the significant linear and quadratic coefficients.