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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