Tophat and Repeated Sequences

[Airwalker810]

My PI and I have been wondering what exactly Tophat does with repeated sequences from a fastq file. Does it merely throw them away, or does it take the read and 'place' it at each location that it appears in the genome? We were going to use the CASAVA pipeline, and I do know that generates a file of repeated sequences that can later be indexed, but Tophat better serves our purposes.

Thanks for the Help.

[Jon_Keats]

Tophat prints the read at each location if it maps to multiple locations so you can end up with 120% mapped. Seems to be a big issue with short (50bp) single end reads, minor when using short paired-end reads so I suspect longer reads in a paired-end format would work better.