Errors in post alignment files

Question: Errors in post alignment files

2.6 years ago by

Canada

Hello. I was trying to perform an alignment of data (Tophat) which had been run through Fast Groomer to database/build Human Dec. 2013 (GRCh/hg38) (hg38). Some of the resultant files had an error message: An error occurred setting the metadata for this data set. with a link: set it manually or retry auto-detection. I tried the latter.

Do you have any suggestions? have there been problems aligning to this build?

Thanks in advance

Joe

rna-seq tophat alignment errors • 844 views

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modified 2.6 years ago by yena.oh • 70 • written 2.6 years ago by joseph.andrews • 20

2.6 years ago by

yena.oh • 70

Canada

yena.oh • 70 wrote:

Hi Joe,

I have also been having similar problems lately. For me, I resolved the issue by "editing attributes" by clicking on the eye icon on the right, and clicking on "auto-detect." Most of the times, the problem was solved. On files where auto-detect didn't work, simply re-running the analysis and retrying "auto-detect" solved the issue.

Hope this works for you as well.

Yena

ADD COMMENT • link written 2.6 years ago by yena.oh • 70

Thanks Yena. Clicking on the link in the error message and clicking "auto-detect seems to have worked. Thank you for your quick reply. Also, do you know what happened to all the videos? I keep getting an error 404 message when I try to view them...

Take care.

Joe Activity on a post you are following on Galaxy Biostar ( http://biostar.usegalaxy.org)

User yena.oh ( http://biostar.usegalaxy.org/u/8720/) wrote Answer: Errors in post alignment files ( http://biostar.usegalaxy.org/p/17475/#17478) :

Hi Joe, I have also been having similar problems lately. For me, I resolved the issue by "editing attributes" by clicking on the eye icon on the right, and clicking on "auto-detect." Most of the times, the problem was solved. On files where auto-detect didn't work, simply re-running the analysis and retrying "auto-detect" solved the issue. Hope this works for you as well. Yena

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ADD REPLY • link written 2.6 years ago by joseph.andrews • 20

2.6 years ago by

yena.oh • 70

Canada

yena.oh • 70 wrote:

By videos, are you referring to visualizing the reads alignment? Once the metadata was set with the warning message gone, visualizing also started worked for me. See if it works!

Yena

ADD COMMENT • link written 2.6 years ago by yena.oh • 70

No. I am referring to the tutorial videos at Galaxy.org. I went Go Galaxy.org, login, click "Help", get a dropdown menu, click "videos". Says the page cannot be found (http 404 error).

Thanks again

Joe Activity on a post you are following on Galaxy Biostar ( http://biostar.usegalaxy.org)

User yena.oh ( http://biostar.usegalaxy.org/u/8720/) wrote Answer: Errors in post alignment files ( http://biostar.usegalaxy.org/p/17475/#17480) :

By videos, are you referring to visualizing the reads alignment? Once the metadata was set with the warning message gone, visualizing also started worked for me. See if it works! Yena

You may reply via email or visit A: Errors in post alignment files

ADD REPLY • link written 2.6 years ago by joseph.andrews • 20

No worries, just found them. They are the Vimeo videos in Help/Support. But the Videos link in the help section is not working...

Joe Activity on a post you are following on Galaxy Biostar ( http://biostar.usegalaxy.org)

User yena.oh ( http://biostar.usegalaxy.org/u/8720/) wrote Answer: Errors in post alignment files ( http://biostar.usegalaxy.org/p/17475/#17480) :

By videos, are you referring to visualizing the reads alignment? Once the metadata was set with the warning message gone, visualizing also started worked for me. See if it works! Yena

You may reply via email or visit A: Errors in post alignment files

ADD REPLY • link written 2.6 years ago by joseph.andrews • 20

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