qTeller MaizeGDB
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Welcome to qTeller for MaizeGDB! BETA


                         

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 will soon host RNA-seq data for multiple genomes; watch this space for new datasets mapped to Mo17, W22, PH207, and more!

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

Visualize expression for one gene as a bar chart, or visually compare expression between two genes as a scatterplot.

Getting started:

  1. Go to the Select Genome drop-down menu at the top left;

  2. Select your genome of interest (right now there is only B73 v4). It will take you to the page of your selected genome.

  3. Then on the left, select either Genes in an Interval, Genes by Name, or Visualize Expression, and follow the directions!

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.