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Examples:

Run Quality Control
	$ baqcomTrimmomatic.R -p 36 -s 2 (paired-end)
	$ baqcomTrimmomatic.R -p 36 -s 2 -z (single-end)
	# -p option is the number of processors to use; 
	# -s option is the number of samples to use at time
	# -z option will run single end analysis
	# More options can be accessed with -h option (baqcomTrimmomatic.R)
	
Run Index and Mapping
Running STAR pipeline
	$ baqcomSTAR.R -t /path/to/reference_genome.fa -g /path/to/reference_annotation.gtf -p 20 -q 3 (paired-end)
	$ baqcomSTAR.R -t /path/to/reference_genome.fa -g /path/to/reference_annotation.gtf -p 20 -q 3 -z (single-end)
	# -t option is the directory where the reference genome is stored (required); 
	# -g option is the directory where the reference annotation is stored (optional but recomended); 
	# -p option is the number of processors to use; 
	# -q option is the number of samples to use at time;
	# -z option will run single end analysis;
	# More options can be accessed with -h option (baqcomSTAR.R -h)
		
Running HISAT2 pipeline
	$ baqcomHisat2.R -t /path/to/reference_genome.fa -g /path/to/reference_annotation.gtf -p 20 -q 2 (paired-end)
	$ baqcomHisat2.R -t /path/to/reference_genome.fa -g /path/to/reference_annotation.gtf -p 20 -q 2 -z (single-end)
	# -t option is the directory where the reference genome is stored (required); 
	# -g option is the directory where the reference annotation is stored (optional but recomended); 
	# -p option is the number of processors to use;
	# -q option is the number of samples to use at time;
	# -z option will run single end analysis;
	# More options can be accessed with -h option (baqcomHisat2.R -h)

Run counting reads
Running HTseq
	$ baqcomHtseq.R -g /path/to/reference_annotation.gtf -q 2 (paired-end)
	$ baqcomHtseq.R -g /path/to/reference_annotation.gtf -q 2 -z (single-end)
	# -g option is the directory where the reference annotation is stored (required);
	# -q option is the number of samples to use at time;
	# -z option will run single end analysis;
	# More options can be accessed with -h option (baqcomHtseq.R -h)
	
Running FeatureCounts
	$ baqcomFeatureCounts.R -a /path/to/reference_annotation.gtf -p 20 -q 2 (paired-end)
	$ baqcomFeatureCounts.R -a /path/to/reference_annotation.gtf -p 20 -q 2 -z (single-end)
	# -a option is the directory where the reference annotation is stored (required);
	# -p option is the number of processors to use;
	# -q option is the number of samples to use at time;
	# -z option will run single end analysis;
	# More options can be accessed with -h option (baqcomFeatureCounts.R -h)