Plots
Hagfish can generate a number of different plots. The most detailed plot of these is:
(Note -there is an older - outdated - script, called hagfish_cplot - which plots only the ECP - mirrored around the x-axis)
A cplot2 plot shows all six coverage plots for any given region. The image below shows a cplot2 plot for a sequence called "S3" starting at position 1 and ending at position 2e5. The image was generated using the following command line:
hagfish_cplot2 -e 2e4 -n 1e4 S3 -S
The plot ranges from position 0 to 20,000 (-e 2e4). The plot it displayed over two separate bands, with 10,000 nucleotides per band (-n 1e4). With the -s parameter it would have been possible to specify a start coordinate for the plot. The left y axis indicates the start position of that specific band, and the type of plot (ICP or ECP). The right y-axis indicates the scale - with a line drawn at the median ok coverage for that complete sequence (not all analyzed sequences). Above the x-axis are the three stacked, inclusive, coverage plots (ICPs): "high" - red, "ok" - green and "low" - blue. Below the x-axis are the three exclusive coverage plots (ECPs), also stacked (but mirrored). The reference sequence contains two small gaps (a stretch of NNNs) inbetween 30k * & 40k, and inbetween 120k and 140k. Gaps are indicated by a yellow backdrop. A score is calculated, and plotted by a thick black line (seeOperation for details on score calculation).
Any region with "sufficient" green ECP coverage (below the y-axis) indicates that that region is completely covered by reads mapping to that region. Any region with "sufficient" green ICP coverage (above the y-axis) indicates that that region is structurally sound, i.e.: based on the read pairs mapped back to the genome
The plot shows two major features...
The same region plotted above is also displayed in the, more compact, plot below:
This plot shows a heatmap, based on the score, and is much better suited to visualize large regions at once.