FastQC Issue with per base nucleotide quality graph

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FastQC Issue with per base nucleotide quality graph

Tan, Justin
Hi,

I am having a problem with FastQC. When I view per base quality, it gives me a strange looking graph:


I am wondering it this is because of a problem with my data? None of my colleagues have seen this before.

Thanks!
Justin




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Re: FastQC Issue with per base nucleotide quality graph

Loraine, Ann
What does it tell you about the number of N's (uncalled bases)?


From: "Tan, Justin" <[hidden email]>
Date: Thu, 28 Mar 2013 10:41:24 -0400
To: "[hidden email]" <[hidden email]>
Subject: [galaxy-user] FastQC Issue with per base nucleotide quality graph

Hi,

I am having a problem with FastQC. When I view per base quality, it gives me a strange looking graph:


I am wondering it this is because of a problem with my data? None of my colleagues have seen this before.

Thanks!
Justin



___________________________________________________________ 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: http://galaxyproject.org/search/mailinglists/

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Re: FastQC Issue with per base nucleotide quality graph

Kreshnik B Ahmeti
In reply to this post by Tan, Justin
If you used the raw illumina fastq data (the txt file generated) file that means that your data quality is very low, the sample has been most likely contaminated. 

you can still run it just to see what it gives you.

Best of luck

Kreshnik
On Mar 28, 2013, at 9:41 AM, "Tan, Justin" <[hidden email]>
 wrote:

Hi,

I am having a problem with FastQC. When I view per base quality, it gives me a strange looking graph:
<per_base_quality.png>


I am wondering it this is because of a problem with my data? None of my colleagues have seen this before.

Thanks!
Justin



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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
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Re: FastQC Issue with per base nucleotide quality graph

Anton Nekrutenko
In reply to this post by Tan, Justin
Justin:

Can you share a history with me via a link (click gear on the top rigt, choose "share or publish" and click "Make history accessible via a link"; then e-mail this link to me). I'll see what is happening.

Tx,

a.



On Mar 28, 2013, at 10:41 AM, Tan, Justin wrote:

Hi,

I am having a problem with FastQC. When I view per base quality, it gives me a strange looking graph:
<per_base_quality.png>


I am wondering it this is because of a problem with my data? None of my colleagues have seen this before.

Thanks!
Justin



___________________________________________________________
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:

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To search Galaxy mailing lists use the unified search at:

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___________________________________________________________
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