Hi,I'm a beginner in RNA-Seq analysis,now I've mapped the short reads with Bowtie,TopHat and other softwares,I'm trying to analyze the mapping efficiency by counting the uniquely mapped reads,spanning junction reads and unmappable reads in different mapping results.But how can I get the information about which one is uniquely mapped,which one is mutiple reads from the SAM format file I get with the softwares?
Thank you for your attention.
Thank you for your attention.
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