September 2018: MaizeGDB qTeller has a new look! A navigation bar at the top with tool drop-down menus makes navigation easier.
27-August-2018: The issue with qTeller due to a server problem has been resolved.
Questions or suggestions? Please let us know on the Contact page.
qTeller is a comparative RNA-seq expression platform to compare expression across multiple data sources in a user-provided gene list or genomic interval, or to visually compare expression between two genes. qTeller has been used extensively in maize and other research.
qTeller has three tools:
Genes in an Interval
Select a chromosomal interval and expression data sources to compare the expression of all the genes in your interval.
Genes by Name
Similar to Genes in an Interval except you provide a list of genes as input instead of a chromosomal interval.
Visualize expression for one gene as a bar chart, or visually compare expression between two genes as a scatterplot.
1. Select your tool of interest at the top navigation bar (Genes in an interval, Genes by name, or Visualize expression), then select your genome of interest from the tool dropdown menu (right now there is only B73 v4 Gramene).
2. Then follow the directions on the tool page!
Frequently Asked Questions (FAQ):
What mapping pipeline does MaizeGDB qTeller use?
For high-throughput mapping of hundreds of SRA runs, we have deviated from the Classic qTeller pipeline by using the STAR mapping algorithm instead of GSNAP. However, we use Cufflinks to count FPKM, just as Classic qTeller does. We map reads against the whole genome, not gene models. Note that as mapping and abundance-counting algorithms continue to evolve, the algorithms we use may also change over time.
What parameters does MaizeGDB qTeller use to map and count reads?
We use default STAR and Cufflinks parameters, and we do not trim our fastq reads before mapping (except where noted).
Who created qTeller?
qTeller was created by Professor James Schnable of the University of Nebraska-Lincoln (Schnable Lab Website) while he was a graduate student at UC Berkeley in Mike Freeling's lab. James was generous enough to allow MaizeGDB to host a version of qTeller on our site.