upload a .begraph file in IGV

[Roberta Carriero]

I have a bedgraph file that I correctly used and visualized in UCSC. Now I want to visualize the same bedgraph file in IGV but when I try to upload the file I get the following error message:      "   Failed to parse line 2: chr5 1 400000 25 Column 3 must be numeric. "

Which could be the problem in your opinion??

Thank you for your help!

[Jim Robinson]

What version of IGV are you using?   Select the Help > About menu to get the version.

I have a bedgraph file that I correctly used and visualized in UCSC. Now I want to visualize the same bedgraph file in IGV but when I try to upload the file I get the following error message:      "   Failed to parse line 2: chr5 1 400000 25 Column 3 must be numeric. "

Which could be the problem in your opinion??

Thank you for your help!

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[Roberta Carriero]

I'm using the version 2.3.6. Do you think this is a problem of version?

[Jim Robinson]

If possible could you try the latest version (2.3.40)?  It is possible, but not likely, that will resolve your problem.  If it does not I will need to see the first few lines of the file.   You can extract them from a terminal on a Mac or linux with a command like this

head -10  yourFile.bedgraph > sample.bedgraph

You can send the sample file, or the entire file,  to igv-team (at) broadinstitute.org,  or attach it to a reply.     Do not copy the contents into the reply (or post) as this can change whitespace.   The problem here has something to do with the whitespace characters separating the columns, so I need to see the actual file.

Jim

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