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4.2.4 Single cell RNA seq

tresor.sc.simu_pcr_num is a Python function in charge of simulating reads with respect to a series of PCR cycles at the scRNA-seq level.

Usage

We take the following command as an example to generate FastQ files with PCR cycles from 1 to 18.

import tresor as ts

for perm_i in range(1):
    print(perm_i)
    ts.sc.simu_pcr_num(
        # initial sequence generation
        gmat=gmat,

        len_params={
            'umi': {
                'umi_unit_pattern': 3,
                'umi_unit_len': 12,
            },
            'seq': 100,
        },
        material_params={
            'fasta_cdna_fpn': to('data/Homo_sapiens.GRCh38.cdna.all.fa.gz'),  # None False
        },
        seq_num=50,
        working_dir=to('data/simu/docs/'),

        condis=['umi', 'seq'],
        sim_thres=3,
        permutation=0,

        # PCR amplification
        ampl_rate=0.9,
        err_route='sptree',  # bftree sptree err1d err2d mutation_table_minimum mutation_table_complete
        pcr_error=1e-4,
        pcr_nums=np.arange(1, 18 + 1, 1),
        err_num_met='nbinomial',

        # PCR amplification
        seq_error=0.01,
        seq_sub_spl_number=200, # None
        # seq_sub_spl_rate=0.333,

        use_seed=True,
        seed=1,

        verbose=False,  # True False
        mode='short_read',  # long_read short_read

        sv_fastq_fp=to('data/simu/docs/'),
    )

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tresor pcrnum_sc \
-cfpn ./tresor/data/amplrate_sl.yml \
-snum 50 \
-permut 0 \
-sthres 3 \
-wd ./tresor/data/simu/ \
-md short_read \
-is True \
-vb True

Attributes

Illustration

Attribute Description
seq_num number of RNA molecules. 50 by default
len_params lengths of different components of a read
seq_params sequences of different components of a read, It allows users to add their customised sequences
material_params a Python dictionary. Showing if cDNA libraries are provided, please use key word fasta_cdna_fpn. The human cDNA library can be downloaded through the Ensembl genome database
ampl_rate float number ranging from 0 to 1
err_route the computational algorithm to generate errors. There are 6 methods, including bftree, sptree, err1d, err2d, mutation_table_minimum, and mutation_table_complete.
pcr_error PCR error rate
pcr_nums list of numbers of PCR cycles to amplify reads
err_num_met the method to generate errors, that is, binomial or nbinomial
seq_error sequencing error rate
seq_sub_spl_number number of subsampling PCR amplified reads. It exists when seq_sub_spl_rate is specified to None
seq_sub_spl_rate rate of subsampling PCR amplified reads. It exists when seq_sub_spl_number is specified to None
sv_fastq_fp folder to save FastQ files
is_seed if seeds are used to simulate sequencing libraries. This is designed to make in silico experiments reproducible
working_dir working directory where all simulation results are about to be saved
condis names of components that a read contains. It can contains an unlimited number of read components
sim_thres similarity threshold. 3 by default
permutation permutation times
mode long_read or short_read
verbose whether to print intermediate results
Attribute Description
cfpn location to the yaml configuration file. Users can specify the atrributes illustrated on the Python tab in the .yml file.
snum number of sequencing molecules
permut permutation times
sthres similarity threshold. 3 by default
wd working directory where all simulation results are about to be saved
md long_read or short_read mode
is if seeds are used to simulate sequencing libraries. This is designed for reproducible in silico experiments
vb whether to print intermediate results

Output

Console

======>simulation completes in 0.02999734878540039s
======>simulation completes in 0.0639963150024414s
======>simulation completes in 0.10599660873413086s
======>simulation completes in 0.15399861335754395s
======>simulation completes in 0.21199822425842285s
======>simulation completes in 0.2799968719482422s
======>simulation completes in 0.3730289936065674s
======>simulation completes in 0.489046573638916s
======>simulation completes in 0.6349985599517822s
======>simulation completes in 1.0400078296661377s
======>simulation completes in 1.649998426437378s
======>simulation completes in 2.403001070022583s
======>simulation completes in 3.8079991340637207s
======>simulation completes in 6.248998165130615s
======>simulation completes in 10.268998861312866s
======>simulation completes in 18.130997896194458s
======>simulation completes in 34.058995962142944s
======>simulation completes in 65.32599782943726s
===>Time: 68.847s
Finished!

Understanding files

The resultant files of the simulated reads are shown as follows.

Image title
Fig 1. Generated FastQ files