Hi Jen,
Thanks so much for your advice.
*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.*
*
*
I ran the Flagstat on my TopHat 's output BAM file. I am now confusing
about the result:
44066574 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
44066574 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ=5)
Note that my RNA-seq data is single-ended sequencing. The raw data for
this sample before mapping with TopHat only has 33174286 reads. My
question is why I have more reads mapped in the BAM file from TopHat's
output? and Does this BAM file contains the mapped reads only ( NOT
non-mapped reads)?
I have also tried the *SAM/BAM Alignment Summary Metrics *tool. This
time I have 25541681 reads from BAM file ( the result seems only show
mapped reads). Is that the number I should expect?
Thank you
Thanh
On Mon, Jul 15, 2013 at 10:41 AM, Jennifer Jackson j...@bx.psu.edu wrote:
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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Jennifer Hillman-Jackson
Galaxy Support and Traininghttp://galaxyproject.org
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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
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use the Galaxy Development list:
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