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Can't load BED file in IGB

Hi,

I'm sorry for asking this simple question but I've tried searching the internet and can't figure out why I can't get this to work!

I have BED files of some ChIP-seq data that has been supplied to me from a company that has done our analysis for us. I'd like to view them in IGB and compare to some other files I have. However, when I load the file and then click the load data button, there's nothing there across the whole genome. These files do however work in the UCSC genome browser. What am I missing here?

Thank you in advance!

igb
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updated by Ram Ram • written by nash.claire nash.claire

do you use the correct chromosome nomenclature (e.g: 'chr' prefix ) ?

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Hi,

Thanks for the reply. I think I just figured out the problem (maybe). The bed file provided for me by the company is not single track, it contains multiple tracks. I know IGV doesn't support multiple tracks and I'm guessing IGB is having the same problem. Is there a way to split the multiple tracks file into single track files? Maybe UCSC can do this I haven't had chance to read and check yet.

• 1 views • link
updated by Ram Ram • written by nash.claire nash.claire

Hello - this is Ann, project lead for the IGB project.

Thank you for your post - I hope you were able to move forward with your analysis.

Also, if you think it would be a good idea for IGB to support loading data from multi-track files, please feel free to suggest it as new feature here: http://bioviz.org/igb/help.html

Just click the "feedback" link. From there, you can quickly enter your request.

Either way, I'll talk with the development team supporting multiple tracks per file.

• 0 views • link
updated by Ram Ram • written by Ann Ann

1 answer

Is there a way to split the multiple tracks file into single track files?

awk '/^track/ {++i;} {f=sprintf("file%d.bed",i); print >> f}' input.bed
• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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