Frequently Asked Questions | Strand NGS

Frequently Asked Questions



What kind of files can I import into Strand NGS?

In the case of Alignment experiments, one can import the sample data in FASTA, FASTQ or tag-count format. In addition, prealigned data in SAM, BAM or Illumina-specific ELAND format can be directly imported for analysis.

Does Strand NGS support alignment of reads?

Yes. Our aligner COBWeb uses a proprietary algorithm based on the Burrows Wheeler Transform method. COBWeb has been optimized to handle both short reads and long reads. It allows an arbitrary number of gaps and mismatches, and handles both single and paired end reads.

How much time will it take to load my data?

Data loading times vary depending on the hardware specifications of the computer you are using. As an example, Strand NGS takes about 3 hours to import 150M reads. You can look up more examples and guidelines on loading, storage, and computation requirements here.

In RNA-Seq experiments, the key difference, compared to other software, is that Strand NGS performs an extra step during import to ensure correct handling of multiply mapping reads. Based on the publication by Mortazavi et. al. at - http://www.nature.com/nmeth/journal/v5/n7/abs/nmeth.1226.html, the best way to handle multiply mapping reads is to distribute them to the genes that they map to in proportion to the number of uniquely mapping reads in those genes. This requires extra processing of the samples when they are imported and hence the comparatively longer import times.

What types of analyses does Strand NGS support?

Strand NGS supports six major NGS experiment workflows including Alignment (DNA, RNA and small RNA), DNA-Seq for whole genome/exome analysis, RNA-Seq for transcriptome analysis, Methyl-Seq to detect methylated cytosines and methylated regions, ChIP-Seq for transcription regulation analysis and Small RNA Analysis for detection and expression analysis of small RNA genes.

How long does the trial period last? What if I need more time to try the software?

The trial period lasts 20 days.
If you need more time, just ask! We will work with you to help you determine if Strand NGS is the right software solution for you.

How can I learn more about the features of Strand NGS?

You can request a demo of the software and one of our Application Scientists will help answer any specific questions you may have. If you have your own data we can help you get started over a webex. We recommend going through the website pages on features pages, video tutorials and recorded webinars for easy understanding of specific analyses. Read the release notes to find out what's new in version 1.5

Can I view multiple genomic regions simultaneously?

A new feature in our genome browser displays multiple genomic regions at different zoom levels simultaneously. The Elastic Genome Browser is particularly useful for analysis of gene fusions, novel splices, and large structural variations.

Is it possible to automate execution of compute intensive jobs?

Strand NGS provides a pipelining feature where multiple workflow steps can be combined into a pipeline and executed in the background. As the pipeline executes in the background, the user could continue working with the tool.

Is it possible to re-import the data files from one experiment to another within Strand NGS?

Import Project can be used to import the exported projects. In addition, during sample loading, the ``Choose Data'' dialog box allows for the quick import of previously imported samples. This is a convenient way to use samples in multiple experiments.

How do I import annotation files?

The annotations for your organism of interest can be directly downloaded from within Strand NGS using the Annotations > Annotations Manager dialog. If you do not find annotations for a particular organism, contact the support team and we will create the necessary annotations for you.

I am having problems getting my data into Strand NGS, what steps should I take?

Before loading the sample data, ensure that it is in the right format. In case of Analysis experiments, the sample data needs to be pre-aligned read data (SAM/BAM/ ELAND format) whereas in case of Alignment experiments, the sample data is the raw read data in FASTA, FASTQ, or tag-count format. In case the problem persists, our technical support team is available around the clock during the business week to assist you.

How do I back-up my data in Strand NGS?

The user can export multiple experiments within a project as a * .tar file that is portable across platforms i.e., Linux, Windows and Mac. However, annotations are not exported.

Can I get the latest version of Strand NGS when I renew the subscription?

Yes. With a valid and a current subscription, you can always download and install the latest version of your product. In addition, product updates are notified as a message when you open the software and are available for download from the Strand server.

Is the license linked to a computer or user?

The license can be activated from only one installation at any time. The OrderID that is provided by Strand will allow a copy of the product to be activated on a single computer. After activation, the OrderID cannot be used to activate a second copy. To use the application on a different computer, the OrderID first needs to be ``surrendered'' on the first computer, which frees up the OrderID that can then be used on a different computer.

What are the minimum hardware requirements to be able to run Strand NGS?

Analysis of samples up to 50 million reads can be done on a regular desktop machine with 32-bit machine with 4 GB RAM, 2 GHz quad-core processor, and about 500 GB of hard disk space. For high coverage whole genome data that need to be aligned, or experiments with large number of samples, a 64-bit machine with 8 GB RAM, two 2 GHz quad-core processors, and about 1 TB disk space should work fine.

What operating systems does Strand NGS support?

Strand NGS is supported on Windows (Windows XP, Windows Vista, and Windows 7), Mac OS X (Leopard (10.5.x), Snow Leopard (10.6.x), and Lion (10.7)), and Linux (Red Hat Enterprise Linux (5.x), and Debian GNU/Linux 5.0) platforms.

What are the licensing options?

The Strand NGS product can be licensed in a number of ways. Most products are licensed through a single-computer license. Alternatively, the product can be licensed with a floating license which allows multiple copies to be installed on different computers, but only one copy can be active on the network at any time.