RNA-seq

RNA-seq experiment analysis code

Fastq analysis pipeline:

RNA-seq_slurm_job.sh

• Aligns FASTQ to specified reference genome
• Sorts and indexes output BAM file to use in genome browser
• Summarizes read counts per gene using featureCounts

Argument options:

• EXPID Custom ID for output files.
• RUNDIR Path to directory to run script and save output in.
• FQ Absolute path to input fastq file.
• GENNAME Reference genome file basename preceded by absolute path to directory containing the reference genome files. The directory must include:
  • FASTA file
  • matching GFF file.

Both files must use the same basename. If an existing Bowtie2 index with a matching basename (Bowtie2's bt2_base) is found in the same directory it will be used; otherwise a new index is built.

• FEAT GFF feature type (featureCounts argument -t). Suggested values:

  • FEAT="gene" for SK1Yue
  • FEAT="CDS" for sacCer3

• ATTR GFF attribute type used to group features (featureCounts argument -g). Suggested values:

  • ATTR="ID" for SK1Yue
  • ATTR="Name" for sacCer3

Example job submission:

sbatch --export EXPID="AH119_3h_SK1Yue",RUNDIR="/scratch/lv38",\
FQ="/scratch/lv38/C8C2NACXX_l03n01_ah119-3-030316.3510000004e291.fastq.gz",\
GENNAME="/home/lv38/Library/SK1Yue/Yue.SK1.genome.nuclear.mito.2micr",\
FEAT="gene",ATTR="ID" ~/Pipeline/RNA-seq/RNA-seq_slurm_job.sh

License

This project is licensed under the terms of the MIT license. See LICENSE file for details.