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  • poisson200
    Member
    • Feb 2010
    • 63
    #1

    Tophat; warning

    I have ran Tophat on 50bp paired-end Illumina data and it generates quite a few warnings as below.

    [Thu Mar 3 09:35:27 2011] Indexing splices
    Warning: Encountered reference sequence with only gaps
    Warning: Encountered reference sequence with only gaps
    Warning: Encountered reference sequence with only gaps
    many more lines of this.

    Is this something to be concerned about? I am using HG19 which was indexed using the latest Bowtie-build;

    bowtie-build version 0.12.7
    TopHat v1.2.0

    Thanks for any tips.

    John.
    Tags: None
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