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Old 04-23-2012, 01:17 AM   #1
dvanic
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Question Reference annotation for mapping (human)?

Question:
Which annotation is best for reference-based/guided mapping and assembly using Tophat/Cufflinks/other tools?

UCSC Comprehensive Gencode11 track, downloaded as a .gtf, has 2072303 records.

ENSEMBL66 [Homo_sapiens.GRCh37.66.gtf] has 2181086 records.

gencode11 (on which ENSEMBL is based(???)) has 2617472 records, of which:
1947538 gencode.v11.annotation.level_1_2.gtf
586834 gencode.v11.annotation.level_3.gtf
74062 gencode.v11.polyAs.gtf
9038 gencode.v11.2wayconspseudos.gtf

Or, what are the pros/cons of using each of them? And what is the actual difference?

Thanks in advance!
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Old 04-24-2012, 07:56 PM   #2
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*bumping up my own post, since this is still relevant*
(Thanks in advance!)
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