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@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@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@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One issue with our screencasts is that Galaxy changes rapidly so they can become slightly out of date.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?

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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@uark.edu https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486# & chandratrihadi2@yahoo.com https://uamail.uark.edu/h/imp/message.php?mailbox=Sent&index=486#

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