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
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