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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!

  • #2
    *bumping up my own post, since this is still relevant*
    (Thanks in advance!)

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