Hello Tao,

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.

Please help us to track new questions and provide prompt help by sending tool and data questions:

1 - to either galaxy-u...@bx.psu.edu or galaxy-...@bx.psu.edu, which are best for most questions. sending to galaxy-b...@bx.psu.edu is mainly reserved for UI bug reports (green bug icon for failed datasets) or for sending shared links to private data.
http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions

2 - with the "to" as the mailing list address "galaxy-u...@bx.psu.edu". When a brand new question is sent with the mailing list as a "cc", it is not tracked.

3 - when a new question is sent as a reply to an earlier thread with a new subject line, it is not tracked. start a new thread for new questions with new subject lines.

4 - please use "reply-all" if you would like more assistance about the same subject to keep the thread consistent for the user community.

Thank you for your help with this!

Best,

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?

Thanks,

tao


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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