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  • Cuffcompare merged.gtf to self not all "="

    I have been working on comparing the results of 20 merged.gtf files to see the differences between each pair of files. When doing this work, I used the following type of command:
    cuffcompare -p 4 -r merged_1.gtf -o ./compare/merged2_vs_1 merged_2.gtf

    This should use merged_1.gtf as the "reference" and compare merged_2.gtf to it. However, I noticed that if merged_1.gtf and merged_2.gtf are switched the results are different. Furthermore, if I compare merged_1.gtf to itself ( merged_1.gtf), not all of the class codes are "=". I actually get something like this:

    "Class_code" #_occurrences_in_.tmap_file
    "=" 215622
    "u" 11040
    "p" 1172
    "c" 1051
    "i" 1707

    How can this be the case? if I compare something to itself, I should expect all class codes to be "=".

    Any thoughts?

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