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dasmoth / dalliance

Interactive web-based genome browser.
http://www.biodalliance.org/
BSD 2-Clause "Simplified" License
226 stars 68 forks source link

Default BAM view should indicate read orientation #67

Closed dasmoth closed 10 years ago

dasmoth commented 10 years ago

Probably needs to be an extension to the __SEQUENCE renderer.

ymen commented 10 years ago

Hi Thomas,

My colleagues and I have also encountered this need in our work, and we modified the __SEQUENCE renderer slightly to color reads at ref bases from + and - strands differently, and the mismatch will be in the colors corresponding to the base (the mismatch mode is more relevant to us, but I believe that might be the case to most people?).

The basic premise was to reproduce what IGV can do (sans the arrow heads). This is what IGV does, pic taken from http://trinityrnaseq.sourceforge.net/analysis/read_alignment_visualization_QC.html screen shot 2014-07-02 at 2 53 25 pm

If you have not already worked on this already, I would be most happy to share this with you with a PR after I check in with my colleagues and clean up a few things (before the end of the week).

Best, Yifei

dasmoth commented 10 years ago

That would be great.

ymen commented 10 years ago

@dasmoth Sorry for the delay. Had to work on a couple of things, but definitely working on this. Will update soon!

dasmoth commented 10 years ago

Many thanks to @ymen for implementing this.