Hello Jiwen, The tool "NGS: Picard (beta) -> SAM/BAM Alignment Summary Metrics" gives a nice set of statistics for paired end data. Hopefully this helps, Best, Jen Galaxy team On 3/7/12 12:35 AM, 杨继文 wrote:

Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance. JIwen

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