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  • no error and no output from cuffcompare

    Dear Guys,

    I just ran cuffcompare, but no output and no errors.

    Here is my command for cuffcompare

    ./cuffcompare -o /Users/puruna/cuffcompare_output/s1 -R -r /Users/puruna/reference.gtf -s /Users/puruna/transcripts_s1.gtf

    And if i use this command

    ./cuffcompare -o cuffcompare -r /Users/puruna/ref.gtf /Users/puruna/cufflinks_output/transcripts_s1.gtf

    then, i got only two output files with .tmap and .refmap, NO .stats, NO tracking, NO combined.gtf

    I don't know what is wrong. I would greatly appreciate any feedback from this community!
    Last edited by hibachings2013; 07-14-2011, 05:53 AM.

  • #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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