DensityMap GUI

Contact

Email address A link to your results will be send at this email address.
Allowed characters: A-Za-z0-9@_.

Input(s) - Output

GFF3 file The GFF3 file describing the sequences.
GFF3 format

(100 Mo max)
Region file A BED file describing sequences regions to plot.
It allow to plot specific regions and not the whole seq.
Exemple of file content:
2L[TAB]100000[TAB]200000
2R[TAB]300000[TAB]450000

BED format

(100 Mo max) (OPTIONNAL)
Output file nameName of the output file without extension.
Allowed characters: A-Za-z0-9_

Data options

Feature
Color scale
Strand

Help

A feature corresponds to an information contained in the third column of a GFF3 file. It can be "gene", "exon", "ncRNA", etc.

The density of a feature (number of covered bases in the sliding window) is represented using a colour scale. Depending on the density of a feature, choose wisely the color scale. For example, the colour scale 11 and 12 are well suited for representing GC content.

You can select the strand on which are computed the densities:

  • +: Compute densities only on strand +
  • -: Compute densities only on strand -
  • both: Compute densities on strands + and -
  • fused: don't consider strand
  • all: + fused -

Colour scales available

scales.svg

Density options

Maximum picture sizeHeigth of the output picture in pixel.
Rounding methodRounding density to upper or lower interger. Floor
Ceil
GC% DensityMapIf the value 0, no density map is drawn for GC content.
Otherwise, colour scale to use for GC% density map.
The sequences must be inclued int the GFF3 file in the ##FASTA section.

Graphical options

TitleTitle to print on the density map.
Allowed characters: A-Za-z0-9, _
Display scaleSelect 0 to remove scale.
Otherwise, select maximum number of ticks ont the scale.
Strand widthWidth in pixel of strands.
Space between strandsSpace in pixel between strands.
Space between chromosomesSpace in pixels between two sequences.
Left marginWidth of left margin in pixel.
Right marginWidth of right margin in pixel.
Top marginWidth of top margin in pixel.
Bottom marginWidth of bottom margin in pixel.
Background color
Orientation of labelsRotation in degrees of labels
Font size

 


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Published on Tuesday, March 29 2016 by Sebastien Guizard