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Old 08-29-2011, 05:22 AM   #1
Location: Israel

Join Date: Oct 2010
Posts: 19
Default Different number of unique reads using TopHat -g

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?
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