MRSA case study example data

<p>### Dataset description<br> <br> This dataset contains fastq files for three Illumina HiSeq runs of an<br> RNA-seq analysis (see Osmundson J et al., PLoS One, 2013;8(10):e76572)<br> <br> This data is used as a case-study for the Tools in Reproducible Research<br> course. We have previously used `fastq-dump` from the `sra-tools` package<br> to download a subsampled set of sequences from the Sequence Read Archive<br> (SRA). However,recently sra-tools has become very unreliable due to some<br> certificate/security issue when downloading from the National Center for<br> Biotechnology Information (NCBI). We have therefore created this dataset to<br> use as an alternative starting point for the course case-study.<br> <br> All three files were generated on the Rackham compute cluster by installing  <br> sra-tools (v.3.0.3) from the bioconda channel:<br> <br> ```<br> mamba create -n sra-tools -c bioconda sra-tools<br> conda activate sra-tools<br> ```<br> <br> then running:<br> <br> ```<br> fastq-dump SRR935090 -X 100000 --gzip -Z > SRR935090.fastq.gz<br> fastq-dump SRR935091 -X 100000 --gzip -Z > SRR935091.fastq.gz<br> fastq-dump SRR935092 -X 100000 --gzip -Z > SRR935092.fastq.gz<br> ```<br> <br> Thus, each file contains a subset of 100,000 reads for each sample downloaded<br> from the original data found in the SRA archive. The original data contains<br> between 76.3 - 176.6 million reads. The idea is to let the students download<br> these subsampled files directly or as part of bioinformatic workflows taught<br> during the course.</p>