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Question: Unable to download bam index file
1
gravatar for cynthiak14
23 months ago by
cynthiak14 • 10
cynthiak14 • 10 wrote:

I have analysed my RNA seq data using TopHat tool under the NGS- RNA seq analysis heading. After the completion of analysis I downloaded the bam dataset but I was unable to download bam index file. Upon clicking on download bam_index, this page is opening :

The usegalaxy.org page isn’t working

usegalaxy.org is currently unable to handle this request. HTTP ERROR 500

Also as I tried to view the file on display with IGV local, display with IGB view and display at bam.iobio.io , The following error is appearing :

Conflict

There was a conflict when trying to complete your request. Error generating display_link: type object 'Bam' has no attribute 'name'

Please help in resolving this issue.
rna-seq tophat bam • 831 views
ADD COMMENT • link •
modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 23 months ago by cynthiak14 • 10
0
gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Issues with BAM indexes is a known problem with certain datasets. Please try resetting the metadata on the BAM dataset. This has resolved the problem for myself and others.

How to:

  • Click on the pencil icon on the top right of the dataset to reach the Edit Attributes form
  • On the first tab, click on the link "Auto-detect"
  • Allow this process to complete, then try downstream tools that use this dataset as an input (including downloading the BAM index)

Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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