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Question: Can't run files successfully using BWA-MEM
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gravatar for stevenmarkgalway
21 months ago by
stevenmarkgalway • 0
stevenmarkgalway • 0 wrote:

Hi

I am currently working on a course project. Using the main galaxy server, I am having issues running any sort of analysis with the fast q files provided. When trying to map the data using the BWA-MEM tool, the required input fields read - No FASTQ Sanger dataset available. I have tried the FASTQ Groomer tool to convert the files to Sanger format, however, downstream analysis on this data produces errors. Any ideas on how I can convert the provided fastq files to fastsanger format that will run successfully using the BWA-MEM mapping tool?

Please feel free to use the following link to look at my history for an example of what I mean.

https://usegalaxy.org/u/stevengalway/h/project

Any feedback would be helpful.

Thank you
bwa • 664 views
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modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by stevenmarkgalway • 0
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gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I can see that the uploaded fastq datasets were directly assigned fastqsanger as a datatype. That is correct and will allow tools to recognize the datasets as appropriate fastq input. Fastq Groomer is not needed for your case.

The downstream tools have failed for other reasons related to problems at Galaxy Main (http://usegalaxy.org) right now. Please try re-running the jobs now. If they fail again, then follow this post for updates on the slow response times and job delays/errors: https://biostar.usegalaxy.org/p/22075/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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