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
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 | . |
