to run scripts on scg3, see Src/commands_to_run.md

otherwise, just run scripts in order:

• Src/s01.merge_fastq.sh

  • merges each fastq, split between 4 lanes, into a single fastq

• Src/s10.fastqc_pre.sh {num_parallel_jobs}

  • quality control before lighter read correction/trimming

• Src/s11.lighter.sh {num_parallel_jobs}

  • or, to submit each file to scg3 individually, each using multiple cores
  • ./s11.lighter_individual.sh {num_cores_per_job}
  • trims/corrects reads

• Src/s12.fastqc_post.sh {num_parallel_jobs}

  • view quality of fastq files after trimming/correction

• Src/s13.star_create_genome1.sh {num_cores}

  • generate reference indexed genome to map to

• Src/s14.star_pass1.sh {num_cores_per_job}

  • note this script will only submit jobs to scg3
  • map

• Src/s15.prep_SJ.sh

  • join de novo splice junctions detected during first mapping

• Src/s16.star_create_genome2.sh {num_cores}

  • create new genome to map to, including detected splice junctions from first mapping

• Src/s17.star_pass2.sh {num_cores_per_job}

  • note this script will only submit jobs to scg3
  • remap to new genome, with de novo predictions from 1st mapping included

• Src/s18.pre_filter_flagstat.sh {num_parallel_jobs}

  • see how the mapping went

• Src/s19.bam_filter.sh {num_parallel_jobs}

  • filter, sort, and index

• Src/s20.post_filter_flagstat.sh {num_parallel_jobs}

  • check bams after filtering

• Src/s22.freebayes_individual.sh {num_parallel_jobs}

• run Src/DEseq.R in R studio session

• run Src/vcf_to_editing_levels.ipynb in jupyter session with python3 kernel

  • recommended: install Anaconda with python 3 from Continuum Analytics
  • required packages to install with conda:
    • pandas
    • scipy
  • install plotly with pip (requires signing up for plotly account)

• All other scripts are just there because I made them, realized I didn't need them, but they work and I'm keeping them here in case I need them later

• Software needed in path

  • GNU Parallel
  • bedtools
  • STAR
  • samtools
  • fastqc
  • lighter
  • R
    • libraries: DEseq2