Question: BED or Interval metadata problem with strand assignment
1
gravatar for zachary.gaber
22 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?

Zachary

ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson24k • written 22 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 22 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 19 months ago by jcs9230
0
gravatar for Jennifer Hillman Jackson
19 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

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: https://github.com/galaxyproject/galaxy/issues/2175

Thanks everyone for reporting the problem, Jen, Galaxy team

ADD COMMENTlink modified 19 months ago • written 19 months ago by Jennifer Hillman Jackson24k
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