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  • scyxr
    Junior Member
    • Sep 2012
    • 2

    Difference between scaffolds.gff3 & top_level.gff3

    Dear all,

    I'm recently trying to annotate my data using GFF file. However, I found two different ref.gff files for human in NCBT ftp site. see as follows:
    ########
    ref_GRCh37.p13_scaffolds.gff3.gz
    ref_GRCh37.p13_top_level.gff3.gz
    alt_CHM1_1.1_scaffolds.gff3.gz
    alt_CHM1_1.1_top_level.gff3.gz
    alt_CRA_TCAGchr7v2_scaffolds.gff3.gz
    alt_CRA_TCAGchr7v2_top_level.gff3.gz
    alt_HuRef_scaffolds.gff3.gz
    alt_HuRef_top_level.gff3.gz
    ################

    those are the file names in GFF directory in the ftp site. I guess I should use ref*.gff3.gz files to do my annotation.
    Can anyone tell me which one is useful for me? ref_GRCh37.p13_scaffolds.gff3.gz or ref_GRCh37.p13_top_level.gff3.gz or else?

    What's the difference between these two?

    Thanks.

    xr

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