Hi Chandra -
If you are still having problems with graphing data, how can we help
more? After SAM-to-BAM, what tools did you use? Were you able to try the
ones that Kelly outlines with any success? Were there problems?
The more specific you are with the steps you have done, the better we
can help guide you towards a useful graph/figure. Maybe you would like
to share a history showing what you have done so far?
Thanks,
Jen
On 7/6/10 11:29 AM, Chandra Trihadi wrote:
Hello,
I am sorry, I did not know about the appropriate address
(galaxy-user(a)bx.psu.edu <mailto:galaxy-user@bx.psu.edu>) for asking.
I tried to map with Bowtie for my illumina single-read data using the
reference genome that I uploaded to the history panel, then filter
SAM, then did SAM-to-BAM. However, the final result did not display
the allignment figure like on the instruction video. Would you mind to
tell me how to obtain the allignment figure or to assembly my illumina
data based on my reference genome?
Thank you.
-Chandra-
Quoting Kelly Vincent <kpvincent(a)bx.psu.edu
<mailto:kpvincent@bx.psu.edu>>:
[Show Quoted Text - 48 lines][Hide Quoted Text]
Hi,
Sorry for the delay in response. In the future, please do send queries
like this to galaxy-user(a)bx.psu.edu
<
https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#>
instead of galaxy-bugs, since it is about using Galaxy rather than a
specific bug in the software.
One issue with our screencasts is that Galaxy changes rapidly so they
can become slightly out of date. In this case, for Illumina data,
there is a tool called "FASTQ Summary Statistics" under Illumina Data
under NGS: QC and manipulation. This is like the "Compute quality
statistics" tool under AB-SOLiD Data. Then, to draw the boxplot, go to
the Graph/Display Data section (not under NGS Toolbox) and choose the
"Boxplot of quality statistics" tool.
Regarding the results of your Bowtie mapping, could you give more
details about what was different from what you were expecting? Did you
make sure that you mapped against the correct genome?
Regards,
Kelly
On Jul 1, 2010, at 5:06 PM, Yohanna Gita Chandra wrote:
Hello Galaxy Team,
I am sorry for asking the same questions for the third time since I
haven't gotten any respons from galaxy team about these problem.
Could you at least tell me why you do not answer my questions yet?
Should I call you?
---------------------------------------------------------------------------
I have illumina sequencing data (single reads), and I am trying to
analyze it.
I listened to the video tutorial on Galaxy about mapping illumina
reads (single end read), and tried to analyze my data based on the
tutorial. However, I found instructions that I could not find on the
Galaxy window.
- In the tutorial, after uploading the data, I should "compute quality
statistic". The "compute quality statistic" is supposed to be under
"GENERIC FASTQ DATA". However, I found it under "AB Solid Data".
Since
my data is Illumina sequencing data, I could not simply do it.
- In the tutorial, if I am done with "compute quality statistic", I
have to do "draw quality score boxplot" that is supposed to be under
"GENERIC FASTQ DATA". However, it is also under "AB Solid Data".
- Then, after uploading my Illumina data, I did FASTQ Groomer, and did
mapping with Bowtie for Illumina, but the result was not like the
example on the instruction video.
Would you mind to tell me what I should do?
Thank you very much in advance.
--------------------------------------------------------------------------------
Yohanna Gita Chandra
University of Arkansas
Fayetteville, AR 72701
Email: ytrihadi(a)uark.edu
<
https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#> &
chandratrihadi2(a)yahoo.com
<
https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#>
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