SeqView Tool

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This tool is the ExpressionPlot genome browser. For RNA-Seq it plots both genomic and junction reads, and for microarray data it plots probe intensities. Specific regions can be specified by genomic coordinates or by feature names. You can highlights to the plots which is useful for identifying specific exons in alternative splicing events. You can also choose from several transcript annotations to show alongside your data. Controls are provided for scrolling and zooming. For convenience, gene level barplots are also plotted on the screen for genes that fall within the requested windows.

seqview Options
Region Use this field to specify either a chromosomal location or gene name, such as the following:
  • chr4:147986490-148001105
  • Tlr7
Highlight A region to highlight can be specified in Highlight. This is useful when examining alternative exons in their context. Type the coordinates as "start-end" without the chromosome. You can highlight multiple blocks by putting more start-end pairs separated by spaces. The first block will appear in a different color than the others to distinguish it (useful for highlight an alternative exon and its flanking exons). Do not include the chromosome, since this

is taken based on the Region field. For example,

 1001000-1002000 1005000-1006000

would highlight two regions, assuming that 1001000-1006000 fell within the window defined by your Region query.

Scroll The Scroll buttons allow you slide the current viewing window.
  • <<< full window to the left
  • << half a window to the left
  • < nudge the window to the left 10%
  • > nudge the window to the right 10%
  • >> half a window to the right
  • >>> full window to the right
Zoom Zoom in or out the requested amount, keeping the center of the current window. The to highlight option

will change the viewing window to be the first highlight block plus a small margin. This is useful to zoom into alternatively spliced exons.

Data set The project you would like to analyze.
Annot. Select which annotation you would like to view alongside your sequencing or array data. Different options may be available depending

on your installation, but the four default are as follows:

  • acembly based on the AceView software, this is the most liberal of the default annotations, and includes many exons with weaker evidence
  • knownGene based on UCSC knownGene set. This is a reliable set of transcripts, although probably not as complete as acembly.
  • ensGene based on a freeze of Ensembl.
  • ens_tRNA contains Ensembl with tRNAs added in. This annotation has good coverage of both coding and non-coding transcripts.
Reverse Complement At high magnification the sequence of the region will be added to the plot. Selecting this option shows the minus strand instead of the plus strand.

(not implemented in version 0.1).

Normalize Read Counts Selecting this option will display normalized read counts (RPM---reads per million) instead of raw read counts. No effect on microarray plots.
Merge Strands/Swap Strands For RNA-Seq data, selecting this option will merge the reads from the two strands. For microarray data, it will swap which strand probes are shown

above and below the annotation.

Group Replicates For microarray data only, this option will group replicate experiments and add error bars to reduce the number of curves. The groups

are based samples which have the same color in colors.txt.

Width Width of the image in pixels
Height Height of the image in pixels
Left Margin If your sample names or transcript names are cut off you can increase the size of the left margin with this option.

Recombining downloaded seqview plots

The annotation and sequence read plots are served as two separate images. The advantage of this system is that the annotation plot, which can be calculated more quickly, will appear first. The disadvantage is that when you try to save the image you will have to save the two parts separately. If you have ImageMagick installed on your system (under ubuntu just run sudo apt-get install imagemagick) then you use the following command to recombine the two images into a single image called single.png:

 montage seqview.R.png annotview.R.png -geometry +0+0 -tile 1x2 single.png