README

You can perform a test of VARUS on this sample data like this:

1. Edit VARUSparameters.txt
   At a minimum the path to the VARUS folder 'Implementation' needs to be set correctly.
   For a quick test of the program, we recommend to set maxBatches to 20.


2a. Run VARUS on a single species like this

../runVARUS.pl --aligner=HISAT --readFromTable=0 --createindex=1\
  --latinGenus=Schizosaccharomyces --latinSpecies=pombe \
  --speciesGenome=S.pombe.genome.fa \
  --logfile=S.pombe.log 2> S.pombe.err\

This command will create a subdirectory Schizosaccharomyces_pombe in the example folder which
will eventually contain
 - a file Runlist.txt with a table with all available RNA-seq runs 
 - a folder genome with the genome index
 - a file VARUS.bam with spliced alignments from all batches and runs

2b. Alternatively, run VARUS on a list of species like this

../runVARUS.pl --aligner=HISAT --readFromTable=1 --createindex=1

This command will read the file 'species.txt' and run VARUS on each species therein.

Please be aware that an untypically high percentage of Schizosaccharomyces pombe sequencing runs in SRA have quality issues.
It is still included as an example because of the small genome.