NYU_bioinformatics_ass2

1. Log on to cluster and create project repository with the following folders:

• ./fastq_files
• ./outputs

2. Submit sbatch job for 'trimgalore.sh'
3. Submit sbatch job for each bt2_sam script:

• bt2_sam_09
• bt2_sam_10
• bt2_sam_11
• bt2_sam_12
• bt2_sam_15
• bt2_sam_16

4. export files from outputs folder on cluster to local machine
5. upload files to IGV and examine each locus (IFNB1, IFIT2, ISG15)
6. Run HighThroughputSeq_Group5.R in RStudio (change paths to local directory)