Hi All,
I used tophat (2.0.9, the latest version) to align RNA-seq data, with option "-g 1" to report one alignemnt for each end of a read. I would suppose the frequency of read's ID is either one (single end mapped) or two (both ends mapped). However, I found many reads were reported multiple times (more than 2).
By further examination using read's ID, sequence and quality, I found these multiple mapped reads were assigned with a wrong ID. For example, the raw data have two reads: read1 and read2, but the name of read2 in the reported SAM files was replace with read1. Does anyone have the same problem?
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