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Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

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[Array Studio Video Tutorial] DNA-Seq Analysis Basics: Getting Started With DNA-Seq Pipeline Analysis And Data QC

Vivian Zhang

Omicsoft Next Generation Sequencing (NGS) analysis includes NGS (next generation sequencing) bioinformatics tools for the entire process, from QC to alignment to post-alignment summarizations and analysis. Array Studio provides a suite of tools to quickly, easily, and reliably process DNA-seq data. In this article, we introduce our tutorial on DNA-Seq analysis pipeline and data QC. We will discuss more on downstream analysis functions in the coming blog(s). 

 

Getting Started with DNA-seq pipeline functions

 

1 Running the DNA-seq pipeline

In Array Studio, users have the choice of either executing each step of the analysis one-by-one, or can use the DNA-seq pipeline function. Our video tutorial will walk you through the functions automatically executed by the standard DNA-seq pipeline, starting with raw reads in .fastq format.

Pipeline.png
DNA-Seq Pipeline. Users have the options to choose to perform analysis steps such as raw data QC, post-alignment data QC, summarize mutation and SNP etc. 

DNA-Seq Pipeline. Users have the options to choose to perform analysis steps such as raw data QC, post-alignment data QC, summarize mutation and SNP etc. 

2 Raw Data QC

If you choose to perform analysis step by step, before aligning your DNA-seq data, you must first perform quality control (QC) on the raw data, to spot common problems like adapter or barcode sequence contamination, degraded quality at ends of reads, or problematic samples. The Array Studio Raw Data QC Wizard reports a number of useful measures of raw NGS quality.

Additional information about how to interpret these functions can be found in the RNA-seq Raw Data QC Analysis video.

3 Map DNA-seq Reads to Genome

Map (DNA-Seq) Reads To Genome is a part of the DNA-Seq pipeline. Users can also align reads independently. In the Advanced tab, the user can set a number of options, including read trimming, adapter stripping and more.

 

4 Aligned Data QC

Array Studio automatically generates an Alignment Report after aligning reads to the genome or transcriptome. Additional alignment statistics can be generated by running the Aligned Data QC module.

 

Additional aligned data QC metrics include: 

1 Alignment Metrics
2 Flag Metrics
3 Profile Metrics
4 Insert Size Metrics
5 Duplication Metrics
6 Strand Metrics
 

 

Please check out our video tutorial Getting Started with DNA-seq pipeline functions for more detailed illustration.