RNA-Seq is a high-throughput sequencing technology used to generate information about a sample’s RNA content. Partek^® Genomics Suite^® offers convenient visualization and analysis of the high volumes of data generated by RNA-Seq experiments.

This tutorial will illustrate how to:

·         Import large next-gen data sets

·         Add attribute data to your files

·         Visualize large next-gen data sets

·         Obtain read counts for each of the transcripts in a database

·         Find transcripts that are differentially expressed among phenotypes

·         Find genes that are alternatively spliced among phenotypes

·         Set up a basic analysis of variance (ANOVA) model

·         Detect nucleotide variations across samples or comparing to reference genome

·         Find nonannotated regions and map it to the genome

Note: the workflow described below is enabled in Partek Genomics Suite version 7.0 software. Please fill out the form at www.partek.com/PartekSupport to request this version or use the Help > Check for Updates command to check whether you have the latest released version. The screenshots shown within this tutorial may vary across platforms and across different versions of Partek Genomics Suite.

Description of the Data Set

In this tutorial, you will analyze an RNA-Seq experiment using the Partek Genomics Suite software RNA-Seq workflow. The data used in this tutorial was generated from mRNA extracted from four diverse human tissues (skeletal muscle, brain, heart, and liver) from different donors and sequenced on the Illumina^® Genome Analyzer™. The single-end mRNA-Seq reads were mapped to the human genome (hg19), allowing up to two mismatches, using Partek^® Flow^® alignment and the default alignment options. The output files of Partek Flow are BAM files which can be imported directly into Partek Genomics Suite 7.0 software. BAM or SAM files from other alignment programs like ELAND (CASAVA), Bowtie, BWA, or TopHat are also supported. This same workflow will also work for aligned reads from any sequencing platform in the (aligned) BAM or SAM file formats.

Data and associated files for this tutorial can be downloaded by going to Help > On-line Tutorials from the Partek Genomics Suite main menu or using this link RNA-seq Data Analysis tutorial files. Once the zipped data directory has been downloaded to your local drive, right click the file and select Extract All. Select the directory you wish to work in and select Extract. The data files are now unzipped and you are ready to proceed with the tutorial.

• For this tutorial, unzip the downloaded files to C:\Partek Training Data\4TissueBamFiles or to a directory of your choosing. Be sure to create a directory or folder to hold the contents of the zip file

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