BWA alignment problem in Galaxy
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 informationsecurityofficer@cmh.edu and expunge this communication without making any copies. Thank you for your cooperation.
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 http://wiki.galaxyproject.org/Support Best, Jen Galaxy team On Wed, Feb 11, 2015 at 10:10 AM, Xiong, Min, <mxiong2@cmh.edu> 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 informationsecurityofficer@cmh.edu and expunge this communication without making any copies. Thank you for your cooperation.
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Maybe its the same issue as posted here? https://biostar.usegalaxy.org/p/3877/#3879 "The datatype for your dataset must be set to fastqsanger" Stef ----- Original message ----- From: "Xiong, Min," <mxiong2@cmh.edu> To: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org> 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 informationsecurityofficer@cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. _____________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ Email had 1 attachment: * Picture1.tif 777k (image/tiff)
participants (3)
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Jennifer Hillman-Jackson -
Stef van Lieshout -
Xiong, Min,