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ha1's Introduction

HA1 Deep mutation scanning

Dependencies

Input files

  • All raw reads in fastq format should be placed in fastq/

Dependencies installation

  1. Install dependencies by conda:
conda create -n HA1 -c bioconda -c anaconda -c conda-forge \
  python=3.9 \
  seqtk \
  flash \
  biopython \
  cutadapt \
  snakemake
  1. Activate conda environment:
    source activate HA1

Calling mutations from sequencing data

  1. Using UMI to correct sequencing errors:
    python script/Dedup_UMI.py fastq NNNNNNN 0.8 2

  2. Counting mutations:
    snakemake -s HA1_pipeline.smk -j 10

ha1's People

Contributors

wangyiquan95 avatar

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