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Sequence composition by cycle plots #503

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 

In pre-ECDP days, we had this very cool plot which showed sequence composition 
counts by cycle.  This can show fragmentation biases that appear at 5' ends, as 
well as RNA-seq random priming biases.  Because reads differ from reference 
genome for bisulfite sequencing, we had a separate version for reference genome 
sequence composition and read composition.  These were very cool, and should be 
resurrected.

Ben.

Original issue reported on code.google.com by benb...@gmail.com on 8 May 2013 at 10:33

GoogleCodeExporter commented 8 years ago 
the csv is still being generated, just a matter of displaying it

Original comment by zack...@gmail.com on 15 May 2013 at 10:05

GoogleCodeExporter commented 8 years ago 
we need to specify how this should be displayed. in the past we had to use a 
weird slider graph since we have 3d data: base (each series) 
,cycle,count,quality.

we can use the same style graph or discuss on how to best display it (for ex: 
not breaking it down by qual)

I will take care of any backend/pipeline part, and natalia can do the ECDP 
interface stuff.

Original comment by zack...@gmail.com on 15 May 2013 at 10:49

GoogleCodeExporter commented 8 years ago 
I've merged in the old display code. its a bit kludgy, but it works...

I had to create a parser, add a new regex for it, and add a new chart type to 
the front end.

Original comment by zack...@gmail.com on 17 May 2013 at 11:03

Attachments:

GoogleCodeExporter commented 8 years ago 
Deployed in eccpgxt-beta

Original comment by natalia....@gmail.com on 17 May 2013 at 11:46

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 23 May 2013 at 5:56

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 4 Jun 2013 at 8:22