It’s pronounced three dot oh

Getting things to “just work” is hard. Getting them to just work and be good is harder. With StrandNGS 3.0, we believe we’ve done both. A quarter year’s labour of love, three dot oh feels different because it is different; it feels good because it is. RNA alignment is faster. If you’re using transcriptome + genome alignment, you … Continue reading “It’s pronounced three dot oh”

Reduce the SNP annotation time by up to 95%

Explore the new script ‘Create Targeted VAL’ in Strand NGS for creating subset of dbSNP database with target regions of interest and run your analysis. This feature reduces your SNP annotation time by up to 95% depending on the target regions of interest. Strand NGS v2.7 has more exciting features. Listed below are few:

Strand NGS v2.7 released

We are excited to share the release of Strand NGS v2.7. This new version comes with several exciting features and enhancements. Listed below are few major enhancements:

Review of selected publications citing Strand NGS

In 2015, we brought in many new features and improvements based on your requirements and feedback. We expanded the Strand NGS epigenomics toolkit by adding the MeDIP-Seq workflow in the v2.5 release. We also added new features like the alignment workflow and SV detection for split reads (watch the webinar), a browser-based copy number variation (CNV) view … Continue reading “Review of selected publications citing Strand NGS”

Webinar on Strand NGS Pipeline Manager for streamlining large scale analysis

This webinar, will highlight the Strand NGS Pipeline Manager feature. In this webinar, you will learn how to customize pipelines and share them with other Strand NGS users. This webinar will give a brief glimpse of an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and … Continue reading “Webinar on Strand NGS Pipeline Manager for streamlining large scale analysis”

Meet us at ASHG 2015!

We are excited to be a part of the Annual Meeting of The American Society of Human Genetics (ASHG) again, this time in Baltimore, Maryland from 6- 10 October 2015. Come and meet us to learn more about our best-in-class next-generation sequencing (NGS) data analysis software Strand NGS and Agilent Technologies state-of-the-art multi-omics analysis software GeneSpring. You can … Continue reading “Meet us at ASHG 2015!”

Integrative RNA and ChIP-Seq analysis of regulatory T-cells

Integrative RNA and ChIP-Seq analysis of regulatory T-cells , a Strand NGS application note describes how integrated multi-omics functionality in Strand NGS was used to find the regulatory role of FoxP3 in T-regulatory and T-helper cells. Learn how the gene expression profiles from RNA-Seq and FoxP3 DNA-protein binding sites from ChIP-Seq are integrated. For mor … Continue reading “Integrative RNA and ChIP-Seq analysis of regulatory T-cells”

Integrated mRNA and microRNA transcriptome analysis in Strand NGS

Using a nasopharyngeal carcinoma case study, this paper highlights the integrated transcriptome analysis capabilities of Strand NGS demonstrating the identification of miRNA – mRNA interactions in regulatory networks. Read the application note on Integrated mRNA and microRNA transcriptome analysis in Strand NGS by Veena Hedatale and Rohit Gupta. For more information, please contact us

Strand NGS v2.5 Release Announced – Know what’s new in it?

Happy to share the release of Strand NGS v2.5. This release comes with many new exciting features and enhancements. Some of the major enhancements include new workflow for MeDIP-Seq analysis, split read alignment, new structural variant caller using split reads, additional RNA QC plots, enhanced RNA-Seq workflow to handle large-scale projects, correlation analysis, meta-data analysis, new … Continue reading “Strand NGS v2.5 Release Announced – Know what’s new in it?”

Mapping RefSeq transcripts to the genome using UCSC

Transcript annotations are extensively used in NGS data analysis. In RNA-Seq, they are used at every step of the pipeline – to map spliced reads against the genome, perform quantification, detect novel exons etc. In DNA-Seq, they are used to predict the effect of variants detected in the sample. Clearly accurate transcript annotations are vital … Continue reading “Mapping RefSeq transcripts to the genome using UCSC”