Hello Thanh,
The tool " NGS: Picard (beta) -> SAM/BAM Alignment Summary Metrics" may
be the tool you are looking for. There are others in this tool group
that added up numbers in BAM or SAM files, and SAMTools has "flagstat",
so you could create you own calculation with one of those, plus a count
on the fastq inputs, and the "Compute" tool, if it is not exactly right.
Are you using the public Main Galaxy instance at
https://main.g2.bx.psu.edu/ (usegalaxy.org) clicking over to connect to
the Genomic HyperBrowser, via web? Or are you doing something else? Can
you give this another try this morning and see if it is working?
Hopefully the first part helped, let us know about the second,
Take care,
Jen
Galaxy team
On 7/14/13 1:47 PM, Hoang, Thanh wrote:
Hi,
I ran TopHat on Galaxy for my RNA-seq data. I want to analyze TopHat's
output files, such as percentage of reads mapped to the genome...but I
am not sure how to do that.
I am also trying to visualize the BAM file by IGB but the following
error message appears : " Failed to authenticate to the server".
Anyone can help with these issues?
Thank so much
Thanh
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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