The tools in the group "NGS: Picard (beta) -> QC/Metrics for sam/bam" can generate statistics, in particular the tool SAM/BAM Alignment Summary Metrics.
Another choice is "NGS: SAM Tools -> flagstat".
If more statistics are needed, then starting with the original FASTQ and the mapping result SAM file, the tools in "Text Manipulation", "Filter and Sort, and Join", and "Subtract and Group" can be used in custom combinations.
This question was almost missed. I was able to locate, format, and send as a new thread to the appropriate mailing list. Hopefully this reply helps or you have already found the tools above.
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Thank you for your help with this!
Jen Galaxy team
Peng, Tao wrote:
Hi jen, after I did TopHat analysis of groomed FASTAQ data, how can I find information on how many total reads went into TopHat? How many reads were removed? How many unique hits to reference genome?
I was trying to prepare a table for presentation and realize that I could NOT find the information in my GALAXY account?