Tim et al, One of the hidden gems in Artemis is the ability to load "User plots". We use this for all sorts of things, including viewing depth/coverage of Illumina reads onto references, highlighting SNPs, and so on. They are a rapid way to visualize new data sets related to the genome sequence.
I have three requests I hope you will consider: 1. Allow user plots to be specified on the command line, similar to how features/entries can be added, but with another symbol (eg. @). This would save plenty of fiddling with menus and file browsers. % art genome.gbk + features1.gff + features2.tab @ userplot1.txt @ userplot2.txt ... 2. Add logarithmic scaling or global clipping to the user plot options. Currently you can have "no scaling" or "dynamic scaling" (based on current viewing window). I guess I would like the option of "global scaling" (set a global min/max to clip to) or "logarithmic scaling" (take log(1+x) for every value). This is because a single outlier value/peak in the user plot data will swamp the detail in the rest of the plot, and although dynamic scaling works around this, it is confusing when you scroll through as the heights aren't graphically comparable from window to window. 3. Add features from DIPS in user plot Currently you can add features based on thresholded peak runs in a user plot. Could you provide the same functionality for dips BELOW a certain threshold? This could be used to mark low coverage zones in a read-depth plot for example. Or perhaps this could be generalized to any "band pass" filter with min and max thresholds. The peaks and dips would be special case where min or max was -Inf or +Inf. Thank you for reading my feedback, --Torsten Seemann --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
