new file:   gatk.pp.slq
    	    Variant discovery pipeline using GATK.

new file:   geno.image2.R
    	    Changes the color of the geno.image functions of R/qtl

new file:   star.map.slq
    	    First alignment to an annotated genome using STAR

new file:   make.sjdb.sh
    	    Makes a merged splice junction database using all sjdb.out.tab outputs from the first star pass. \
	    This is a pre-process to create an SJ.2pass.sjdb to implement the 2pass method from Engstrom et al. 2010.

new file:   star.2pass.genome.slq
    	    Generate a STAR genome for the 2nd pass.  Uses the SJ.2pass.sjdb from the previous step, and the \
	    available genome annotation.

new file:   star.2pass.slq
    	    Second pass alignment using STAR

new file:   star.cuffX.slq
    	    Runs cufflinks on the Aligned.out*.bam. Independently of pass.

new file:   star.htseq.slq
    	    Runs htseq-count on the Aligned.out*.bam. Independently of pass.