Simulation#

Take the dataset SRR12060401 as an example to generate simulated data with mimic UMIs.

  • Download dataset

wget https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12060401/SRR12060401

  • Open the dataset using fastq-dump

fastq-dump --split-3 SRR12060401

  • Configuration

    Or

    • Create a file and copy below

[Paths]
result_dir = ./D9_sim_test/

[SourceInputData]
input_file = ./data/SRR12060401.fastq

[General]
num_workers = 60
chunks_num = 100

[GraphSetup]
high_freq_thre = 4
max_error_freq = 4

[Simulation]
min_freq = 4
min_read_count = 30
substations = True
indels = False
error_rate1 = 0.09
error_rate2 = 0.02
sim_random_state = 42

  • Run

noise2read -m simulation -c D9_simi.ini