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README
allp.ec.sh
rept.config.txt
rept.pipeline.sh
sim.par
subsampler.py
trin.sh

README

The empirical dataset can be recreated by running the subsampler.py script on the Trinity Mouse data available from http://sourceforge.net/projects/trinityrnaseq/files/misc/MouseRNASEQ/mouse_SS_rnaseq.50M.fastqs.tgz/download
The simulated dataset is available at http://dx.doi.org/10.5061/dryad.km540


All assemblies can be downoaded at http://dx.doi.org/10.6084/m9.figshare.725715

The scripts contained in this folder can be used to recreate analysis

**sim.par: This is the parameter file needed by the Flux Simulator. Running this should produce 30 million 100nt paired-end simulated Illumina reads
**subsampler.py: see above. Useful for subsampling an Illumina dataset
**allp.ec.sh: This is the code for running the AllPathsLG error correction module
**rept.config.script: This is the config file that reprile requires. Settings indicated by the test are to be optimized for each specific dataset, using instructions provided below, or more comprehensively by the readme contined in the Reptile download
**trin.sh: this is the code for running a basic Trinity asssembly

**rept.pipeline.sh: This file contains a list of the commands that will allow for the production of Reptile error correcte reads.It includesa adaptor and quality trimming steps using Trimmomatic.


####
####Reptile Parameter Optimization
####


Step 0: set MaxBadQPerKmer to something between 7-10 for 100nt reads.
Step 1: set kmer size. Perhaps best to match assembly kmer, though this is only a hunch.
Step 2: set MaxErrRate to something low, perhaps 1% or 2%

Step 3: run the seq-analy script

Step 4: open the quality histogram file
	Find lowest quality score such that the value in the third column is >= .80. Update  'QThreshold' setting
	Highest quality score such that the value in the third column is <= .20. Update 'Qlb'

Step 5: Rerun after changine those settings

Step 6: open the k-mer histogram file
	'T_expGoodCnt': set to two times the value of the first column in histogram where the third column is approximately .95
	'T_card': set to the value of the first column in the histogram where value in the second column is the second peak (maximal) value.

Step 7: Do the error correction using the reptile-omp script.