|Date:||Tuesday, October 16, 2012,|
|Time:||01:00 pm – 04:00 pm|
ONLINE PARTICIPATION: People unable to attend the tutorial in 575 Walter can use UMConnect to view the tutorial online. Please register as usual. Registered users will receive an email with the meeting information within 24 hours of the workshop start date. To participate in the hands-on portion of the workshop, users must have access to an ssh command line tool (Putty on Windows, Terminal on Mac). Please visit http://www.oit.umn.edu/umconnect/ to ensure that your system meets the minimum requirements necessary to participate in this webinar.
RNA-seq is rapidly supplanting microarray analysis as a means of comprehensively profiling gene expression due to rapidly decreasing costs and unparalleled gene isoform resolution capabilities. In the last two years, the so-called “Tuxedo Suite” of tools (i.e., bowtie, tophat, cufflinks and cummeRbund) have become ubiquitous standardized software packages to analyze this rich and complex data. During the same time period, the Galaxy Bioinformatics framework has evolved to become an invaluable front end to these and many other analysis packages enabling researchers without in-depth programming knowledge and commandline familiarity to carry out their own data analysis.
In this hands-on tutorial, participants will perform standard best- practices analysis with sample Human RNA-seq data from the Human BodyMap project to illustrate from start to finish the use of RNA-seq to replace microarrays. This will include sample QA/QC, mapping via tophat, assessing mapping statistics, visualizing data in trackster and IGV, computing differential expression via cuffdiff, and doing some sample comparisons via PCA analysis and clustering.
Familiarity with using Galaxy is strongly recommended.
|Prerequisites:||Familiarity with using Galaxy is strongly recommended|