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  • Cuffcompare - no output, no warnings

    Hi,

    I am running cuffcompare after making transcripts.gtf and merging those for each of the two conditions I wish to investigate. I am running without a gtf reference (I want to see the difference between running with and without -g ref.gtf makes). I am using cuffcompare 2.0.0:

    cuffcompare -o ~/cufflinks/cuffComp/no_gtf/ -V -s /data/ref.gtf
    /cufflinks/N_merged.cufflink_no_gtf/transcripts.gtf
    /cufflinks/P_merged.cufflink_no_gtf/transcripts.gtf

    I get no output at all. Verbose gives me the following:

    Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
    Prefix for output files:
    Processing qfile #1: /cufflinks/N_merged.cufflink_no_gtf/merged.gtf
    Loading transcripts from /cufflinks/N_merged.cufflink_no_gtf/merged.gtf..
    Processing qfile #2: /cufflinks/P_merged.cufflink_no_gtf/merged.gtf
    Loading transcripts from /cufflinks/P_merged.cufflink_no_gtf/merged.gtf..
    Tracking transcripts across 2 query files..
    Cleaning up..
    Done.

    This takes ~30 seconds. Tried with transcripts.gtf also. Also tried with another set of gtf files. Running with a ref.gtf gives:

    <list of duplicates>
    61 duplicate reference transcripts discarded.
    ..reference annotation loaded
    Prefix for output files:
    Processing qfile #1: /cufflinks/N_merged.cufflink_gtf/merged.gtf
    Loading transcripts from /cufflinks/N_merged.cufflink_gtf/merged.gtf..
    2134 redundant cufflinks transfrags discarded.
    Found 11538 transcripts with undetermined strand.
    Processing qfile #2: /cufflinks/P_merged.cufflink_gtf/merged.gtf
    Loading transcripts from /cufflinks/P_merged.cufflink_gtf/merged.gtf..
    1145 redundant cufflinks transfrags discarded.
    Found 11302 transcripts with undetermined strand.
    Tracking transcripts across 2 query files..
    Cleaning up..
    Done.


    Any advice or help would be very much appreciated

  • #2
    Because you gave a output directory while cuffcompare asked for a output prefix. Which means you give a blank prefix to cuffcompare.
    So the outputs that are supposed to be output_prefix.combined.gtf are now just .combined.gtf.
    And in a lot of linux-like systems, .* file (a file starts with dot) is treated as a hidden file.
    Check your output directory and you probably will see them there, hidden.

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