The Long-read RNA-seq quality control software.
Project description
LQC: Long-read RNA-seq Quality Control
The Long-read RNA-seq quality control software.
LQC is used to generate quality control summary report for mapped SAM/BAM files of long-read RNA-seq data (PacBio, Oxford Nanopore). LQC provides detailed information about the indels, mismatches and splicing sites in the BAM files, which provides a good reference for evaluation for the sequencing quality of the long-read sequencing data.
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Dependencies
The LQC software was developed with python3, which demands several python packages.
- python3.6+: with os, sys, argparse, re, functools, collections, multiprocessing, shutil.
- numpy: 1.10+
- pandas: 1.0+
- matplotlib: 2.0+
- pysam: 0.16+
Bootstrap 5.1.3 is used by the final html report. Network access is required to load the css file.
Installation
It's advised to install the software into a virtual environment.
Create virtual environment:
conda create -n lqc
conda activate lqc
Or:
virtualenv ~/.env/lqc
source ~/.env/lqc/bin/activate
From github
Download from github:
git clone https://github.com/gxiaolab/LQC
cd LQC
Install the package:
python setup.py install
From pip
pip install lqc
Usage
LQC accepts SAM or BAM file with cs tag (generated with --cs options by minimap2), or MD tag. If the SAM/BAM file has only MD tag, a genome fasta reference file is required as well to get the splicing information. Since cs tag included the splicing site information, a genome fasta reference is not required by SAM/BAM with cs tag.
usage: lqc [-h] -b BAM_FILE [--genome-fasta GENOME_FASTA] [-o OUTPUT_DIR] [--output-cs]
[--output-pickle] [-c [CONTIG ...]] [-t THREAD] [--log-level LOG_LEVEL] [--version]
The Long-read RNA-seq quality control software.
optional arguments:
-h, --help show this help message and exit
-b BAM_FILE, --bam-file BAM_FILE
input bam file, with cs tags, sorted and indexed
--genome-fasta GENOME_FASTA
path of genome fasta file
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
directory to store output files
--output-cs output processed cs tags
--output-pickle output pickle file of results
-c [CONTIG ...], --contig [CONTIG ...]
contigs to be analyzed
-t THREAD, --thread THREAD
threads to be used in calculation
--log-level LOG_LEVEL
logging level (default INFO): [DEBUG, INFO]
--version show program's version number and exit
The output directory should be empty to allow the storage of output files.
Output
By default, four kinds of output files will be generated by LQC:
summary table, figures, html report, and pickle file to restore python
statistic objects. And with the --output-cs
option, the processed cs
tag information of the BAM file will also be outputed. Similarly, with
the --output-pickle
option, the result objects will be outputed into
one pickle file, which can be used for further analysis.
Summary table will be stored in the table subdirectory of the output directory. Figures will be stored in the fig subdirectory of the output directory.
Processed cs tag file has six columns: read name, contig, low, high, cs mark, cs value.
The LQC will also generate a html report for checking of the BAM file qualities.
Screenshot of LQC report:
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