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IDT UMI workflow

Snakemake workflow for processing CAPPSeq data sequenced using IDT's UMIs. Note that this workflow requires paired-end FASTQ files which have been prepared using IDT's UMI structure

Configuration

  1. Download the workflow: git clone https://github.com/morinlab/idt_umi_workflow
  2. Edit the sample file under config/samplelist.tsv with your samples of interest
  • This will be a 3-column config file containing sample_id, path_to_R1_fastq, path_to_R2_fastq
  • Use "#" to comment out lines
  1. Edit the workflow config file under config/cappseq_umi_config.yaml for your project's parameters
  2. Create a conda environment containing snakemake version 7 or newer, and activate that environment
  3. Run the workflow using snakemake --use-conda -s cappseq_umi_workflow.smk -j <number_of_threads>

Workflow

CAPPSeq_workflow

Results

  • Final processed BAM files (collapsed and error corrected using UMIs) can be found under 99-final/
  • Final QC report can be found under Q9-multiqc