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      Hello, I have chip seq data aligned with macs 2, in BED format.
      I'm being unable to see the peaks in IGB... When I open in UCSC, this singe track actually appears as multiple tracks and I saw that maybe this might be the problem...

      https://www.biostars.org/p/160075/

      Is there a way to solve this issue?

      Reporter: giuliana
      E-mail: gcc32@case.edu

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          ann.loraine Ann Loraine added a comment -

          Reply:

          "Thank you for getting in touch!

          It sounds like the file is a multi-part BED file, with separate sections that beginning with their own separate "track" lines. But without seeing the file, I cannot be sure about that. If this would not be violating confidentiality, perhaps you could send me the file so that I could take a look?

          If there are indeed separate sections with their own "track" lines, then maybe the best solution would be to separate those sections into individual files. Then you could load them one-by-one, and each would be placed into its own track.

          This would be a bit tedious to do by hand, and it is something you would want to do many times, we could create a simple IGB App to automate this process. Basically, it would allow you to select the file, click a button that says "Convert", and then the newly converted files would appear on your computer, available for you to open them in IGB. We already have at least one App that converts one type of file format into another, so this would not be too hard to implement, I think. But we would need an example file to work with.

          I look forward to hearing from you on this, and thank you for using IGB!

          Warm regards,

          Ann"

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          ann.loraine Ann Loraine added a comment - Reply: "Thank you for getting in touch! It sounds like the file is a multi-part BED file, with separate sections that beginning with their own separate "track" lines. But without seeing the file, I cannot be sure about that. If this would not be violating confidentiality, perhaps you could send me the file so that I could take a look? If there are indeed separate sections with their own "track" lines, then maybe the best solution would be to separate those sections into individual files. Then you could load them one-by-one, and each would be placed into its own track. This would be a bit tedious to do by hand, and it is something you would want to do many times, we could create a simple IGB App to automate this process. Basically, it would allow you to select the file, click a button that says "Convert", and then the newly converted files would appear on your computer, available for you to open them in IGB. We already have at least one App that converts one type of file format into another, so this would not be too hard to implement, I think. But we would need an example file to work with. I look forward to hearing from you on this, and thank you for using IGB! Warm regards, Ann"

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            • Assignee:
              ann.loraine Ann Loraine
              Reporter:
              support Support (Inactive)
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