Introduction
This page presents images from the IGB software showing a variety of data types and data sets. Most of these images are from data sets created in the Loraine Lab. Some examples (e.g., the tiling array examples) come from data harvested from the Gene Expression Omnibus.
Visualizing RNA-Seq reads aligned onto a genome
This image from IGB shows short read sequences aligned onto the Arabidopsis A_thaliana_Jun_2009 (TAIR9) genome. The track above the Coordinates track presents part of two Arabidopsis gene models, with sequence data loaded. Note how the reads seem to support two alternative splicing variations in the overlapping gene. Also note the nucleotide differences between the aligned reads (upper track) and the reference sequence.
Visualizing output from TopHat and BowTie
The image below shows output from TopHat and BowTie, programs that align short reads from Illumina sequencing experiments onto a genome. The top two tracks are from a BED format file that TopHat creates in which each line of the BED file represents a splicing choice and the score field indicates the number of reads that supported that choice. The two floating graphs (red and green) are from WIG files the programs produce that summarize the number of reads covering individual regions. In this particular experiment, the control sample (green) produced many more reads than the treatment sample (red), and so the fact that there are more reads overall in the treatment (red) sample tells us this gene is up-regulated under the treatment.