Package: glh-test
IntroductionMODER(Molecular Outlier DEtection from Rna sequencing assays)is a comprehensive and user-friendly toolkit to detect aberrant gene expression, alternative splicing, and allele specific expression from multiple samples. MODER is built on python3 and easy to use. Users only need to provide a list of bam files, and MODER will do all complicated, error-prone processing automatically and return all three kinds of outliers (gene~sample pairs).FrameworkDocumentationDocumentation can be found onhereDependencybioinfomatics softwaresamtools:bedtools:bcfools:If you have installedconda, you can easily install samtools and bcftools by following command.conda install -c bioconda samtools
conda install -c bioconda bedtools
conda install -c bioconda bcftoolsIf your are working with Debian-based linux system, it's convenient for you to install samtools and bctools by package manager -- aptsudo apt install samtools
sudo apt install bedtools
sudo apt install bcftoolspython packageInstallationFor install MODER, you can use git to pull down all code to your linux system. Make sure samtools, bcttools and all dependency third-party python libraries has been installed, then you call use it easily by a python script namedmoder.py. Look forUsgaeto get more information about how to use this program.git clone -b singleTissue https://github.com/Xu-Dong/mOutlierPipe.gitUsagemode argumentoptiondescription--expressionassign mode to analysis Gene Expression data--splicingassign mode to analysis Splicing data--aseassign mode to analysis ASE datawe provide three arguments to decide which analysis pipeline will be run, and all three analysis pipeline will be run if you don't provide any option of these, :lookmodule1for more information of expression pipeline.lookmodule2for more information of splicing pipeline.lookmodule3for more information of ase pipeline.basic argumentoptiondescription-i , --inputtxt file with all input bam file path (required)--gtfgenome annotation file of GTF format (required)-o , --outputdirectory to store all resulting files(optional and default output dir is current directory)-p , --parallelparallel number(optional and default value is 1)--thresholdthreshold of z_score, used to get outliers which abs value larger than threshold defined by this arguments(optional and default value is 2)more arguments and their usage, you can refer tofeatureCounts,peer,leafcutter,SPOT,gtfToGenePredandgenePredToBedyou can run all these pipeline by command as follow:python moder.py -p 8
	--input file_path.txt
	--gtf genome_annotation.gtf
	--vcf example.vcf.gz
	--variation Vg_GTEx_v8.txt
	--tissue MSCLSK
	--threshold 2module1: Expression Data AnalysisThis module is designed to analysis gene expression data. The basic command line arguments and descriptions as follows. More available parameters refer toRNA-SeQCandPEERcommand line argumentsoptiondescription--expressionassign mode to analysis Gene Expression data-i , --inputtxt file with all input bam file path (required)--gtfgenome annotation file in GTF format (required)-o , --outputdirectory to store all resulting files(optional and default output dir is current directory)-p , --parallelparallel number(optional and defalut value is 1)--thresholdthreshold of z_score, used to filter results' value larger than threshold(optional and default value is 2)running examplepython mOutlierPipe.py --expression 
	--parallel 8 
	--input file_path.txt
	--gtf sample_annotation.gtf
	--threshold 2module2: Splicing Data AnalysisThis module is designed to analysis splicing data. The basic command line arguments and descriptions as follows. More available parameters refer toleafcutter,SPOTandPEERcommand line argumentsoptiondescription--splicingassign mode to analysis Splicing data-i , --inputtxt file with all input bam file path (required)--gtfgenome annotation file in GTF format, used to translate cluster id to gene id (required)-o , --outputdirectory to store all resulting files(optional and default output dir is current directory)-p , --parallelparallel number(optional and default value is 1)--thresholdthreshold of z_score, in splicing analysis pipeline, the value of z will be translated to p(optional and default value is 0.0027)running examplepython mOutlierPipe.py --splicing 
	--parallel 8
	--input file_path.txt
	--gtf genome_annotation.gtf
	--threshold 2module3: Allele Specific Expression AnalysisThis module is designed to analysis allele specific expression data. The basic command line arguments and descriptions as follows. More available parameters refer tophASERcommand line argumentsoptiondescription--aseassign mode to analysis ASE data-i , --inputtxt file with all input bam file path (required)--gtfgenome annotation file in GTF format, used to translate cluster id to gene id (required)--vcfVariant Call Format file, include variation information about the genome (required)--varianttissue-specific estimates of genetic variation in gene dosage (required)-o , --outputdirectory to store all resulting files(optional and default output dir is current directory)-p , --parallelparallel number(optional and default value is 1)--thresholdthreshold of z_score, in ase analysis pipeline, the value of z will be translated to p(optional and default value is 0.0027)running examplepython mOutlierPipe.py --ase
	--parallel 8
	--input file_path.txt
	--gtf genome_annotation.gtf
	--vcf sample.vcf
	--variant Vg_GTEx_v8.txt
	--threshold 2