Tophat uniquely mapped reads

[mrfox]

I have just posted two questions but this time I would make it simpler and clearer. If I do not use "-g1" when running Tophat(i.e., allow multi-hits), then how can I identify uniquely mapped reads? My understanding is they are mapped reads with "NH:i:1", where NH is "Number of reported alignments that contains the query in the current record". Am I right?
Thank you.

[wisense]

Yes,you are right.When the 5 column of the bam file is 255,it also means it is an uniquely mapped read.

[rahilsethi]

NH:i:1 does not give uniquely mapped reads when TopHat run under default settings

No, when running TopHat "NH:i:1" will not report uniquely mapped reads when run with default settings. This is because under default settings max no of reported primary alignments are 20 even when it is actually greater than 20. When I looked for max value of NH:i: in the output of whole transcriptome sequence it is 20. So some reads, in reality may contain more than 1 alignment NH:i: will give only the no. of reported alignment and in this case only primary alignments are reported. NH:i:1 for some reads may still give you 1 if only primary alignments are 1, even if the total alignments is greater than 1