DEMINING: a stepwise computational framework to directly detect expressed DNA and RNA mutations in RNA deep sequencing data (DEMINING).
Version: 1.0 2023/12/15
Author: Zhi-Can Fu (fuzhican@picb.ac.cn)
git clone git@github.com:fuzhican/DEMINING.git
cd DEMINING; unzip DEMINING.zip
conda env create -f environment.yml
conda activate ~/DEMINING_env
Usage: DEMINING -f Function -1 Path_of_fastq1 -2 Path_of_fastq2 -o Output_path -n Output_name -c Path_of_config_file -t Maximum_threads -g Genome_build_version [ -s Site_list_file -b BAM_file ]
Arguments:
[-f Function, "Read_mapping", "Variant_classification" or "All_steps"(default "All_steps")]
[-1 Path of fastq1]
[-2 Path of fastq2]
[-o Output directory (default current directory)]
[-n Output name]
[-c Path of config file]
[-t Maximum_threads]
[-g Genome build version, "hg38" or "mm10"]
[-s Site list file (No column name, only required when Function == "Variant_classification")]
[-b BAM file (Only required when Function == "Variant_classification")]
[-h show this help message and exit]
[-v version for DEMINING]
-
Distinguish DNA and RNA mutations directly from RNA-seq fastq files
./DEMINING -f "All_steps" -1 Test_data/HG00145_chr22_R1.fastq.gz -2 Test_data/HG00145_chr22_R2.fastq.gz -o DEMINING_test -c Test_data/DEMINING_test.conf -n HG00145_chr22 -t 2 -g hg38
DEMINING_test/
├── HG00145_chr22_DEMINING.tsv # Predict result
└── HG00145_chr22_DEMINING_tmp # Internal files of DEMINING
-
HG00145_chr22_DEMINING.tsv
Field Discription Site Genomic coordinates DeepDDR_rawScore Probability of RNA mutation from DEMINING DeepDDR_DM(DNA_mutation)_or_RM(RNA_mutation) Predict label of site (DM: DNA mutation; RM: RNA mutation)
Fu, Z.C.#, Gao, B.Q.#, Nan, F., Ma, X.K., and Yang, L.* (2024). DEMINING: a deep learning model embedded framework to distinguish RNA editing from DNA mutations in RNA sequencing data.
Copyright ©2023 Fudan University. All Rights Reserved.
Licensed GPLv3 for open source use or contact YangLab (liyang_fudan@fudan.edu.cn) for commercial use.
Permission to use, copy, modify, and distribute this software and its documentation for educational, research, and not-for-profit purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice in all copies, modifications, and distributions.
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