Question: Tophat
0
Jennifer Hillman Jackson ♦ 25k wrote:
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-user@bx.psu.edu or galaxy-dev@bx.psu.edu, which
are
best for most questions. sending to galaxy-bugs@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_discussi
ons
2 - with the "to" as the mailing list address "galaxy-
user@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
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support