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  • Workflows
    • By Workflow
      • Automated Virtual Cloning
      • Sanger Sequence Assembly
      • Multiple Sequence Alignment
      • Pairwise Sequence Alignment
      • PCR Primer Design
      • PCR Site-Directed Mutagenesis
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      • Whole Exome/Genome Sequencing
      • RNA-Seq Alignment and Analysis
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RNA-SEQ ALIGNMENT AND ANALYSIS

Accurately align RNA-Seq data of any size and sequencing technology against a reference sequence, then perform extensive, in-depth analysis, from differential gene expression to mRNA isoform visualization. PRICING REQUEST WEBINAR

Use Lasergene Genomics to get the whole picture of your RNA-Seq data.

RNA-seq is currently one of the leading technologies available for exploring the transcriptome, which is crucial to connecting the information about a genome with its functional protein expression. But RNA-Seq data analysis can prove to be a challenge for many researchers as the applications for this technology are quite broad. Lasergene Genomics quickly and easily aligns any size RNA-Seq data set — from bacteria to human— against a reference genome, and then offers extensive analysis of the aligned data so that you can explore in-depth. Perform statistical analyses of differential gene expression using RPKM or DESeq2, easily identify genes of interest using comprehensive filtering tools, utilize gene ontologies to identify the relationship between genes with known biological functions, easily visualize and analyze mRNA isoforms for gene expression analysis using Sashimi plots, see variants detected in the sequencing data, and more. We don’t always know what we are looking for when we begin analyzing RNA-Seq data. Lasergene Genomics makes it easy to explore points of interest so that you can get the whole picture of your data set.

RNA-Seq alignment and analysis in 4 simple steps

RNA-Seq Step 1

Step 1

Set up and run alignment

RNA-Seq Step 2

Step 2

Filter to find genes of interest

RNA-Seq Step 3

Step 3

Perform statistical analyses

RNA-Seq Step 4

Step 4

Visualize results

computer

Learn more about RNA-Seq Alignment and Analysis

Resources | Tutorials | FAQs | Benchmarks | Citations | User Guide

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Resources

Please see our resources below for more information on RNA-Seq alignment and analysis.

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Automating Workflows in DNASTAR’s Lasergene Genomics Suite for High-Throughput Applications

View Poster

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Considerations for Next-Gen Sequence Assembly and Analysis Software Selection

Read White Paper

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Cloud Assemblies for NGS Sequences

Watch Webinar

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RNA-Seq with Enhanced Isoform Analysis

Watch Webinar

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Combined NGS Analysis Webinar

Watch Webinar

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Is Open Source NGS Software for You?

Read Blog Post

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Q&A: NGS Sequence Assembly on the Cloud

Read Blog Post

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Free NGS Assembly and Alignment for Genomic Sequencing Data

Read Blog Post

Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about RNA-Seq alignment and analysis.

Combined NGS Analysis for RNA-Seq and ChiP-Seq Data

See how to use Lasergene Genomics to easily combine RNA-Seq and ChiP-Seq projects for integrated analysis and visualization.

Creating Gene Sets and Comparing in the Venn Diagram

See various ways to filter and create gene sets of interest, then compare the gene sets in the Venn diagram in ArrayStar.

Using Sashimi Plots in GenVision Pro

This quick tip video demonstrates how to interpret Sashimi plots in GenVision Pro.

Visualizing Genes and SNPS from ArrayStar in GenVision Pro

This quick tip video demonstrates how to visualize groups of genes or SNPs from ArrayStar in GenVision Pro.

FAQs

Which RNA-seq analysis methods are used to identify differentially expressed genes?

BioConductor’s DESEQ2 and EdgeR statistical packages can be used to identify differentially expressed genes. Start by using the SeqMan NGen wizard to specify a Bioconductor statistical package as the normalization method, then perform the assembly. Open the finished assembly in ArrayStar to perform downstream analysis.

How do I visualize mRNA isoforms?

To visualize mRNA isoforms, use GenVision Pro’s Sashimi plots. Isoforms can also be analyzed in text format using ArrayStar’s Isoform table.

Can I align sequence data to mRNA sequences?

Yes, RNA-seq assemblies can be run with either mRNA reference sequences or whole genome reference sequences.

What types of read technology are supported for an RNA-Seq alignment?

Illumina, 454, Ion Torrent, and Sanger.

Can I combine RNA-Seq data with ChIP-Seq results?

Yes. Lasergene Genomics enables you to combine and analyze multiple NGS projects from different workflows, including RNA-Seq, ChIP-Seq, CNV and miRNA.

Where do I get the reference sequence for aligning RNA-seq data?

If your organism of interest is a commonly-studied species, you can simply press a button on a SeqMan NGen wizard screen to download a DNASTAR genome template package or a reference sequence from NCBI.

If I have multiple samples, can I run them as separate assemblies?

Yes. In the SeqMan NGen wizard screen where you browse to your sample data, check the box next to “run multi sample data as separate assemblies.” You will be prompted to group and name each experiment, which you can do automatically or manually. If desired, you can also define replicate sets on the same screen.

What types of post-alignment RNA-seq analysis options are available?

By using ArrayStar for your RNA-seq data analysis, you can combine gene expression data, isoform info, detected variants, annotations and ontology in a single project. You can compare gene expression values between experiments using scatter plots, heat maps, and line graphs. In addition, you can identify genes, isoforms and variants of interest through simple or advanced filtering based on signal, annotation values or many other options.

Benchmarks

Lasergene Genomics Reference-Guided Genome Alignment Benchmarks
Data SetSequence TechnologyCoverageAssembly Time
Yeast Genome (ERX009559)*Illumina22X2 Minutes
Yeast Genome (srx1484451)*Ion Torrent22X3 Minutes
Drosophila Genome (SRX1961013)*Illumina23X23 Minutes
Human Exome (SRR701474)*Illumina81X53 Minutes
Mouse Rna-seq (SRX2013345)*Ion Torrent ProtonNA1.3 Hours
Human Rna-seq (SEQC-UHRR & Brain)IlluminaNA1.6 Hours
Rice Genome (Srx179262)*Illumina34X1.6 Hours
Human Exome (SRX1873412)*Ion Torrent Proton162X3.9 Hours
Human Genome (SRP000239)*Illumina36X23 Hours

Citations

Evaluation of Ribosomal RNA Removal Protocols for Salmonella RNA-Seq Projects
Bhagwat, Z. Ying and A. Smith, Advances in Microbiology, Vol. 4 No. 1, 2014, pp. 25-32. doi: 10.4236/aim.2014.41006.

Cstf2t Regulates expression of histones and histone‐like proteins in male germ cells
Grozdanov, P. N., Li, J. , Yu, P. , Yan, W. and MacDonald, C. C. (2018), Andrology, 6: 605-615. doi:10.1111/andr.12488.

Clubroot resistance gene Rcr6 in Brassica nigra resides in a genomic region homologous to chromosome A08 in B. rapa
Chang, A., Lamara, M., Wei, Y. et al. BMC Plant Biol 19, 224 (2019) doi:10.1186/s12870-019-1844-5.

CD63, MHC class 1, and CD47 identify subsets of extracellular vesicles containing distinct populations of noncoding RNAs
Kaur, S., Elkahloun, A.G., Arakelyan, A. et al. Sci Rep 8, 2577 (2018) doi:10.1038/s41598-018-20936-7

Apicidin Attenuates MRSA Virulence through Quorum-Sensing Inhibition and Enhanced Host Defense
Parlet, Corey P. et al. Cell Reports, Volume 27, Issue 1, 187 – 198.e6.

Low-phosphate-selected Auxenochlorella protothecoides redirects phosphate to essential pathways while producing more biomass
Park S-H, Kyndt J, Chougule K, Park J-J, Brown JK (2018). PLoS ONE 13(6): e0198953. https://doi.org/10.1371/journal.pone.0198953.

In-Frame Indel Mutations in the Genome of the Blind Mexican Cavefish, Astyanax mexicanus
Daniel Berning, Hannah Adams, Heidi Luc, Joshua B Gross. Genome Biology and Evolution, Volume 11, Issue 9, September 2019, Pages 2563–2573, https://doi.org/10.1093/gbe/evz180

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Brenda Oppert, USDA ARS CGAHR

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