Question: BED or Interval metadata problem with strand assignment
gravatar for zachary.gaber
19 months ago by
United Kingdom
zachary.gaber80 wrote:

Hello, I'm having a problem with many bed files I upload or create in Galaxy. Galaxy keeps identifying a strand column, even when there is no strand column and I cannot uncheck the strand column box. This is a huge problem because when it missassigns the strand column, the files become worthless - any downstream operations I try with them just comes back as empty. I keep trying to manually unclick the strand column box but nothing I do ever seems to change it - Galaxy keeps insisting that column 1 is the strand column! I've seen at least one other person had this problem but I never heard of a fix being identified.

The only workaround I've found is that it has something to do with renaming files - if I leave the bed files with whatever name Galaxy gives them by default, they seem to work properly but if I rename the files then the strand column box gets checked and the files become useless. However, this is a poor workaround as I often do some pretty complex analyses and it gets confusing when all my file names are the default galaxy names.

Has anyone else had this problem or hopefully found a solution?


ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson23k • written 19 months ago by zachary.gaber80

I am having exactly the same issue, even with files that I have not renamed. Using Safari.

ADD REPLYlink written 19 months ago by robert-cornell0

Still a bug. I surrendered and workaround by changing the value of all strands to "+" using the text manipulation tool for changing column values.

ADD REPLYlink written 16 months ago by jcs9230
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson23k wrote:


Problems with BED metadata is a known issue that is still being worked on. This ticket is tracking the problem and includes a workaround for some use cases:

Thanks everyone for reporting the problem, Jen, Galaxy team

ADD COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson23k
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