OmicScript pipeline for DNA-Seq data analysis

From Array Suite Wiki

DNA-Seq pipeline

As we shown in Oshell, you can virtually run any OmicSoft function (e.g., mutation detection, fusion detection, etc.) in Oshell, and even run them in a batch mode in cluster and Amazon Cloud if needed. Below, I will give one example of OmicScript pipeline for DNA-Seq data analysis.

Data analysis modules

DNA-Seq pipeline in OmicSoft Project Environment.

Description of each pipeline function

OmicSoft Function Description Note
NewProject Create the OmicSoft project enviornment .
OpenProject Open exisiting OmicSoft project enviornment .
NgsQCWizard The QC Wizard is a quick and easy way to run multiple QC commands simultaneously. Available options are Basic statistics, Base Distribution, Quality BoxPlot, K-Mer Analysis and Sequence Duplication. .
MapDnaSeqReads Align to genome reference using OmicSoft Aligner .
AddMappedDnaSeqReads Add genome mapped DNASeq reads if user decides to use other aligners .
DnaSeqQCMetrics Report alignment QC Metrics, such as mapping statistics, Duplication rate and other, see DNASeqQCMetricsTable for details .
MapFusionReads Fusion detecting based on the alignment of fusion junction spanning reads .
ReportPairedEndFusionGenes Report paired end fusion based on inter-transcript read pairs .
SummarizeMutation Mutation detection .
SummarizeMatchedPairVariation Mutation detection based on tumor–normal pair to identify germline, LOH and somatic mutations. .
AnnotateMutation Annotate with gene coding info and dbSNP .
SummarizeCnv Summarize copy number variation in small bins. .
SegmentNgsCnv Generate copy number segmentation results from Log2Ratio data. .
ExportView Export all figures and report tables to files .
BamTools /Action=Bas Create BAS file for quick genome browser loading For OmicSoft GenomeBrowser only
SaveProject Save the OmicSoft project enviornment Recommended to save the environment after each step
CloseProject Close the OmicSoft project enviornment .