FASTQ to FASTA tool

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FASTQ to FASTA tool

Omri Finkel
Hello, I've been trying to convert a 454 metagenomic dataset I've downloaded from genbank SRA database, from FASTQ to FASTA. 
The operation doesn't seem to work on the Galaxy web interface. 

Help?

thanks,

Omri

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Omri Finkel
The Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Givat Ram 91904
tel: 02-6584862
e-mail: [hidden email]



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Megablast parser

Andre Pitaluga
Hi all,
I ran a megablast on 454 data, downloaded it convert into zip file, upload it again and tried to run the parser but got this message: "<a href="javascript:void(0);">megablastSRR036068.zip
An error occurred running this job: The zipped uploaded file contains inappropriate content"

Does anyone got the same issue? am I doing something wrong? Please if some one could give me any idea I appreciate!

Thanks
André Pitaluga

Oswaldo Cruz Institute


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Re: Megablast parser

Anton Nekrutenko
Andre:

Can you explain in more detail?

Thanks,

anton
galaxy team


On Jun 9, 2010, at 10:49 AM, Andre Pitaluga wrote:

Hi all,
I ran a megablast on 454 data, downloaded it convert into zip file, upload it again and tried to run the parser but got this message: "<a href="javascript:void(0);">megablastSRR036068.zip
An error occurred running this job: The zipped uploaded file contains inappropriate content"

Does anyone got the same issue? am I doing something wrong? Please if some one could give me any idea I appreciate!

Thanks
André Pitaluga

Oswaldo Cruz Institute


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Re: Megablast parser

Anton Nekrutenko
Andre:

Why are you doing steps 4 - 7 if you already have tabular output in Galaxy? What are you trying to do?

Thanks,

anton




On Jun 9, 2010, at 11:35 AM, Andre Pitaluga wrote:

Dear Anton,
Thank you for your fast replay. 
I have a 454 data uploaded on Galaxy, which I performed the following steps:

1-  Edit the attribute converting to 454 quality file
2 - Convert Fastq to fasta
3 - Ran Megablast
4- Download the tabular output
5 - conver locally to xlm format
6 - zip and upload the file
7 -ran the parser

Could you please give me some help?
What I am doing wrong?
Thank you,
André


Oswaldo Cruz Institute


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Re: Megablast parser

Anton Nekrutenko
Andre:

"Filter and Sort" section on Galaxy tool pane has the tools that will help you. However, if you tell me a bit more about what you are trying to do I can probably be a bit more specific.

Thanks,

anton
On Jun 9, 2010, at 12:02 PM, Andre Pitaluga wrote:

Hi Anton,
Those steps I used because the parser request the following: "Blast XML output must be uploaded to Galaxy in zipped form".
There is anyway to perform the parser using the megablast tabular data already located at Galaxy?
Thank you again,
André

Oswaldo Cruz Institute


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Re: FASTQ to FASTA tool

Daniel Blankenberg
In reply to this post by Omri Finkel
Hi Omri,


Can you provide an example of how this is not working? If you received a job error (red dataset) can you click on the blue bug link for that dataset and report the error? Or you can share your history with us and we can take a look.


Thanks for using Galaxy,

Dan


On Jun 9, 2010, at 6:20 AM, Omri Finkel wrote:

Hello, I've been trying to convert a 454 metagenomic dataset I've downloaded from genbank SRA database, from FASTQ to FASTA. 
The operation doesn't seem to work on the Galaxy web interface. 

Help?

thanks,

Omri

--
Omri Finkel
The Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Givat Ram 91904
tel: 02-6584862
e-mail: [hidden email]


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[hidden email]
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Re: FASTQ to FASTA tool

Daniel Blankenberg
Hi Omri,

Thanks for reporting this issue.  There were two different FASTQ to FASTA tools loaded in Galaxy.  The one located under the 'Convert Formats' tool menu was only designed to handle Solexa formatted FASTQ files, which was different from the tool located under 'NGS: QC and manipulation' --> 'Generic FASTQ manipulation' --> 'FASTQ to FASTA converter' which works on any FASTQ variant.  Sorry for this confusion, we've made the tool which works on any variant the default tool in both locations.  

You can use the tool that is now present in either location to convert your file to FASTA.  Unfortunately, in this case, the re-run button will not work and you will have to manually re-select the tool from the left-hand menu.

Thanks for using Galaxy,

Dan



On Jun 9, 2010, at 12:45 PM, Omri Finkel wrote:

Hi Dan,

Thank you for your response. I clicked the bug link (green on my screen..) and sent out the report. I can share my workflow, but all I have done with this particular file was upload it and then try to convert it. 

Here is the error message:
An error occurred running this job: fastq_to_fasta: Invalid quality score value (char '/' ord 47 quality value -17) on line 12

gzip: stdout: Broken pipe


Cheers,

Omri

On Wed, Jun 9, 2010 at 7:29 PM, Daniel Blankenberg <[hidden email]> wrote:
Hi Omri,


Can you provide an example of how this is not working? If you received a job error (red dataset) can you click on the blue bug link for that dataset and report the error? Or you can share your history with us and we can take a look.


Thanks for using Galaxy,

Dan


On Jun 9, 2010, at 6:20 AM, Omri Finkel wrote:

Hello, I've been trying to convert a 454 metagenomic dataset I've downloaded from genbank SRA database, from FASTQ to FASTA. 
The operation doesn't seem to work on the Galaxy web interface. 

Help?

thanks,

Omri

--
Omri Finkel
The Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Givat Ram 91904
tel: 02-6584862
e-mail: [hidden email]


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galaxy-user mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user




--
Omri Finkel
The Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Givat Ram 91904
tel: 02-6584862
e-mail: [hidden email]




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