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  • convert gtf -> ucsc gene track format

    hello,

    does anybody know a script to convert a gtf-file to the ucsc gene track files needed for RUM index generation.

    alex (dobin): why is gencode UCSC FAs (chr1, chr2, ...) based???

    I need a file in the following format (like downloading a track from ucsc):
    - name (ENST000000001)
    - chrom (chr1, chr2, ...)
    - strand (-,+)
    - exonStarts (zero-based: xxx,yyy,zzz,)
    - exonEnds (one-based: aaa,bbb,ccc,)

    I want make an index for RUM using Gencode 15 annotation,
    but unfortunately Gencode is UCSC HG19-FA based.

    for generating an index for RUM you need either ENSEMBL FAs (1,2,...) and the corresponding GTF files

    or

    UCSC HG19 FAs (chr1, chr2, ...) and UCSC gene tracks (name, chrom, strand, exonStarts (zero based), exonEnds (one based))

    thank you,

    dietmar

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