baraaorabi / ltr-vis Goto Github PK

• Why limit to few reads? 
• Presenting a use-case scenario would help the audience understand the vis purpose
• Change the colors of the bases
• Don't use a color for the match segment, especially the same color as one of the bases.
• Add a vertical axis that follows the mouse to track position across the tracks
• Remove x-axis marks from lower tracks and add a single shared x-axis
• Hide insertion size labels and show them upon mouse hover.

• Colors look unpolished
• Fix the bugs
• The order: is having the gene/genome sequence in the middle of the detailed view?
• Select min bubble size (hide less than X)
• What would happen for >999 (four digit or five digit) insertions? Some reads can be "ultra long" and show such insertions
• There are also some overlaps between insertion bubbles. Maybe consider allowing the user to drag the bubbles away?
• I have a 1M base gene. Can I use this vis tool to see reads on that gene? Are there possible simplifications that can help me with that? Allowing the user to hide or shrink a large interval into a contracted three-dots. Also, if the gene is too large, would I be able to zoom in? Or will the view be restricted to fit the screen size? This might render the gene features invisible.

Overview

• Add ref track
  • Motifs of interest (backend)
• Add prefix/suffix/infix tracks
• Add match block alignment score (scale of 1-5 from worst to best)
  • Color of match blocks indicates alignment score
• Add start/end on read for all ins blocks

Detail:

• Qual is height
• Mismatch bases are colored

Other:

• Fuse deleted ranges
• Target switching (backend)
  • also frontend
  • hide detail view for large intervals