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Old 04-10-2015, 09:14 PM   #1
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Location: Singapore

Join Date: Oct 2014
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Default Clarification "nearest_ref_id" in cummeRbund

Hi to all,

I was dealing with querying cummeRbund as a part of the Tuxedo pipeline. In the isoforms table, there is a column called nearest_ref_id.
I want to clarify my understanding. I think that the authors of the program specifically "coined" the term "nearest_ref_id" to indicate that the cuffdiff2 generated transcript was similar to the description of the transcript in the gtf file (in my case the flybase gtf file).
If I think correctly, this means that FBtr... numbers mentioned against the isoform_id indicate that, the isoform_id represents the flybase transcript (especially when class_code is "="), when flybase transcript descriptor is available for comparison.
What about when the class_code is other than "=" ?


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