TODO

- add support for htseq-count. this will be used for edgeR and other methods later.
    - you will need to define library type (strandedness and side)
    - you will need to extract the feature (eg. type=gene) and attribute (eg. --idattr=gene_name)
        - it would be ideal to extract the options from the first few features and show them as example
- get proper reads for testing under example_notebooks/reads/raw
- get value for project number in job scripts
- make hisat indexes for all the available genomes
- define a quality score threshold and use it to block or continue RNAseq (in master_qsub)

- Defining replicates of a sample fails under specific circumstances:
    -- If the names are too simlar: MG1655-a, b, c and MG1655-1, 2, 3 would be grouped under the same sample with 6 replicates.
    -- If the only difference in groups is the sample ID: reads from MG1655-a_S11, MG1655-a_S12, MG1655-a_S13 would be considered under one replicate.