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04-23-2012, 01:17 AM
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#1 |
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Member
Location: Sydney, Australia Join Date: Jan 2012
Posts: 61
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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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04-24-2012, 07:56 PM
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#2 |
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Member
Location: Sydney, Australia Join Date: Jan 2012
Posts: 61
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*bumping up my own post, since this is still relevant*
(Thanks in advance!) |
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