TIMELAPSE RAW WORKFLOW IN AFTER EFFECTS

I currently create time lapse footage in Premiere Pro CS5.  My basic workflow is to import dslr frames into Lightroom and convert to DNG.  I do all my image enhancement/correction in Lightroom and then export JPEG files.  I then use the JPEG files to make my movie sequence in Premiere Pro and output to the AVID DNxHD format.
From what I understand I can do a sequence directly from RAW files in After Effects and then output the DNxHD format directly from the raw sequence.  I assume this will provide a high level of image quality.  Is that true?   Would it be dramatically noticeable?  Thanks !!

That is correct, unfortunately we can't keyframe raw settings mid-sequence.  However I've had very good results with using separate imports of the same sequence, using different raw settings, then blending/dissolving, (in AE), the sequences to achieve nice results.  I don't use LR much, but that could work... not sure.  Tiffs are unwieldly, at least that's been my experience.  Work with your raws.
My belief is in digital realm, why not have as much quality as possible!  You never know where your footage might find a home - AND don't forget, the 4k+ rez of dslr, well 5DmkII and the like, allows you to make zooms and pans within your sequence.  As bogiesan mentions there are deflicker and other apps/scripts available, I guess I'm just more hands-on.  I've deflickered footage using my above method with excellent results.  Some might find it tedious, but it bloody works.
Delve deep in Timescapes.org, there gems there, and everything you need to know about time lapse.
Here's a recent effort of mine - actually my first, (after many tests, trials and tribulations) http://vimeo.com/23830325

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