Adding work that was done previously on cream-ce.

- bam2fastq_LP6005857-DNA_A01.qsub and bam2fastq_LP6005857-DNA_A01.unmapped.qsub (Converting BAM to FASTQ using Picard. I think this was very slow at that point or something caused it to fail)
- bam2fastq_bamtools_LP6005857-DNA_A01.unmapped.qsub (Converting BAM to FASTQ using using bamtools. I think this is what we used to at the end.)
- create_random_genome.qsub, create_random_genome.sh and validate_random_genome.qsub (Create a random genome from the 24 samples)
- download_homo_sapiens_UCSC_hg19_from_illumina_igenomes.qsub (Downloading the exact reference used in the alignment)
- extract_mapped_LP6005857-DNA_A01.qsub and extract_unmapped_LP6005857-DNA_A01.qsub (Extracting reads)
- fastqc_LP6005857-DNA_A01.mapped.qsub, fastqc_LP6005857-DNA_A01.qsubm fastqc_LP6005857-DNA_A01.unmapped.qsub, flagstat_LP6005857-DNA_A01.qsub, qualimap_LP6005857-DNA_A01.qsub, samstat_LP6005857-DNA_A01.qsub (QC plots and stats. The qualimap script failed on cream-ce but I haven't tried it on hex)
- genomeCoverageBed_LP6005857-DNA_A01.qsub, idxstats_LP6005857-DNA_A01.qsub and generate_coverage_bed.sh (Calculate coverage and generate BED track for Galaxy)
For testing purposes a BED track is generated on chr1 only. Slight modifications are needed to do it on the whole genome.