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.
Thank you.
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