Real_UMI

Take the dataset SRR1543694 as an example to generate real sequencing data with UMI-based ground truth.

• Download dataset

wget https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1543694/SRR1543694

• Open the dataset using fastq-dump

fastq-dump --split-3 SRR1543694

• Configuration

  • Download it from SRR1543694.ini

  Or

  • create it by yourself and copy the following contents

  [Paths]
  result_dir = ./
  
  [SourceInputData]
  input_file = /path_to_data/SRR1543964.fastq
  
  [General]
  num_workers = -1
  
  [GraphSetup]
  high_freq_thre = 4
  max_error_freq = 4
  
  [RealUMI]
  umi_in_read = True
  umi_start = 0
  umi_end = 12
  non_umi_start = 24
  group_read_number = 10
  read_edit_dif = 2
  

• Run

noise2read -m real_umi -c SRR1543694.ini