modified:   create.igenome.sh
	    Uses environmental variables to indicat the location of the iGenome.
	    For MacOS sort -V is not present. Thus, sorting is done differently

new file:   bwa.map.slq
    	    This is a shell script that alings DNA-seq .fastq sequence reads in a
	     directory.using the Burrows-Wheeler Aligner (http://bio-bwa.sourceforge.net/).
	     Both *R1* and *R2* fastq need to be present in the same directory.
	     The number of files analyzed is controled by the `sbatch --array`
	     argument at submittion.  Script was designed for the SLURM scheduler
	     version 2.6. Compatibility with later versions of SLURM is unknown.

new file:   tophat.map.slq
    	    This is a shell script that aligns RNA-seq .fastq sequence reads in a
	     directory using Tophat2 (http://tophat.cbcb.umd.edu/). In addition
	     the script sorts the .bam files by name using `samtools sort -n`
	     and by position `samtools sort`, and runs cufflinks to assembl
	     transcripts.  Lastly, the script submits a script that indexes,
	     and runs htseq-count on the .bam files.  The separation was done
	     due to the number of processors used. The processees in idx_htseq.slq
	     use only single processor.
	     The number of files analyzed is controled by the `sbatch --array`
	     argument at submittion.  Script was designed for the SLURM scheduler
	     version 2.6. Compatibility with later versions of SLURM is unknown.

new file:   idx_htseq.slq
    	    This is a shell script that inherits all environment variables from
	     tophat.map.slq, and runs `samtools index` on .bam files, and
	     htseq-count for counting reads in all known transcripts.
	     The script also intended to run picard-tools CollectRnaMetrics, and
	     htseq-qa (quality assesment) but the latter two have failed. Thus,
	     currently commented out.

new file:   cuff.analysis.slq
    	    This is a script first runs cuffmerge to merge all .bam files
	     from a given experiment, and then runs cuffdiff.
	     The script is not verified, as cuffmerge and cuffdiff returned
	     all read counts as 0 (zero) and was left.
Merge branch 'master' of https://github.com/RodrigoGM/mouseomics