BWA alignment problem in Galaxy

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BWA alignment problem in Galaxy

Xiong, Min,

Hi,

When I use BWA alignment, FASTQ file can't be detected. What reason cause it?

The attached file contains figure from galaxy, you will see I have good fastq file which can be reported by FastQC.

 

Thanks

 

Min Xiong, Ph.D.

Post-doctoral Fellow

Shui Q. Ye Lab  Group

Division of Experimental and Translational Genetics

Department of Pediatrics

Children's Mercy Hospital

2401 Gillham Road

Kansas City, MO 64108

 

 



Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital’s Information Security Officer via return electronic mail at [hidden email] and expunge this communication without making any copies. Thank you for your cooperation.

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Re: BWA alignment problem in Galaxy

Stef van Lieshout
Maybe its the same issue as posted here?
 
"The datatype for your dataset must be set to fastqsanger"
 
Stef
 
----- Original message -----
From: "Xiong, Min," <[hidden email]>
Subject: [galaxy-dev] BWA alignment problem in Galaxy
Date: Wed, 11 Feb 2015 12:10:12 -0600
 

Hi,

When I use BWA alignment, FASTQ file can't be detected. What reason cause it?

The attached file contains figure from galaxy, you will see I have good fastq file which can be reported by FastQC.


Thanks


Min Xiong, Ph.D.

Post-doctoral Fellow

Shui Q. Ye Lab  Group

Division of Experimental and Translational Genetics

Department of Pediatrics

Children's Mercy Hospital

2401 Gillham Road

Kansas City, MO 64108



 

Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital’s Information Security Officer via return electronic mail at [hidden email] and expunge this communication without making any copies. Thank you for your cooperation.
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Re: BWA alignment problem in Galaxy

Jennifer Hillman-Jackson
In reply to this post by Xiong, Min,
Hello,

You probably need to reassign the datatype to be "fastqsanger", but double check the quality score scaling first. You FastQC run will be part of this. Our wiki has the details here, sections 2.9 & 2.10.1 

Best,
Jen
Galaxy team

On Wed, Feb 11, 2015 at 10:10 AM, Xiong, Min, <[hidden email]> wrote:

Hi,

When I use BWA alignment, FASTQ file can't be detected. What reason cause it?

The attached file contains figure from galaxy, you will see I have good fastq file which can be reported by FastQC.

 

Thanks

 

Min Xiong, Ph.D.

Post-doctoral Fellow

Shui Q. Ye Lab  Group

Division of Experimental and Translational Genetics

Department of Pediatrics

Children's Mercy Hospital

2401 Gillham Road

Kansas City, MO 64108

 

 



Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital’s Information Security Officer via return electronic mail at [hidden email] and expunge this communication without making any copies. Thank you for your cooperation.

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--
Jennifer Hillman-Jackson

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