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  • Different number of unique reads using TopHat -g

    Hi,
    I am running TopHat (v1.1.4) on single end reads (72bp)
    I run TopHat several times, each changing only the '-g/--max-multihits' option: default (40), 2, 1
    [I also use the --butterfly-search option in all cases]

    After each run, I count the number of uniquely mapped reads in the output accepted_hits.bam by counting read ids that appear only once in the file.
    I expect to get the same number of unique maps in each run, since it's the same data, however, I get a different number for each run. for example:
    (-g 1): 23,177,858
    (-g 2): 26,223,890
    (-g 40): 29,025,648

    Any idea why this happens?
    Thanks!

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