Question: Is this a .bed file? If so, why is it not importing into IGV properly?
0
gravatar for biohack92
4.2 years ago by
biohack92150
United States
biohack92150 wrote:

I was given a file that the user said was a .bed file at it is formatted as follows:

 

chr1
17000
17200
10.1134
chr1
17200
17400
10.1134
chr1
17400
17600
10.1134
chr1
17600
17800
0
chr1
17800
18000
7.58506
chr1
18000
18200
12.6418
chr1
18200
18400
20.2268
chr1
18400
18600
5.05671
chr1
18600
18800
5.05671
chr1
18800
19000
7.58506
chr1
19000
19200
0
chr1
19200
19400
12.6418

The user wants to import it into Broad Institute's Integrative Genomics Viewer (IGV) but I'm having issues importing the file. Can someone explain what the issue may be? Thank you.

igv genomics bam bed • 1.2k views
ADD COMMENTlink modified 4.2 years ago by EagleEye6.3k • written 4.2 years ago by biohack92150
1
gravatar for Dan D
4.2 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

Two things i'm not sure about:

  1. Your data as posted in your answer are in the form of an HTML table. BED data should be tab-delimited.
  2. I'm not sure what that fourth column is supposed to be. You only need the first three columns. The rest are optional, and the fourth is "name". Odd to have floating point numbers as names, and the numbers are pretty low for typical BED score values.

If you can tell us what exactly the issues are when trying to import the BED data into IGV, that might give us more information with which to help you.

ADD COMMENTlink written 4.2 years ago by Dan D6.8k

@DanD, it's actually tab-delimited. I had a formatting issue while transferring from excel file. Fourth column is a normalized value that my lab is developing.

ADD REPLYlink written 4.2 years ago by biohack92150

"I had a formatting issue while transferring from excel file"

That might be the key to the problem. Make sure you are using newline character as record delimiter, not carriage return (as in MacOS) or newline+carriage return (as in Windows).

ADD REPLYlink written 4.2 years ago by dariober10k
1
gravatar for Matt Shirley
4.2 years ago by
Matt Shirley9.0k
Cambridge, MA
Matt Shirley9.0k wrote:

This is more accurately a bedGraph file: http://genome.ucsc.edu/goldenpath/help/bedgraph.html

The distinction is simply that the fourth column encodes a value instead of a feature name. IGV places too much weight on file extensions, so try changing the name of the file from .bed to .bedgraph.

ADD COMMENTlink written 4.2 years ago by Matt Shirley9.0k
1
gravatar for Alex Reynolds
4.2 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

I was given a file that the user said was a .bed file

Trust no one! This is especially true with data coming from Excel users! 

Run cat -et foo.bed | head and make sure it is tab-delimited, and that each line has one proper newline character. Your data should look something like this:

chrN^I123^I345^I0.1234$
...

Tabs will be shown as ^I characters, and newline characters as $. If you have other stuff there, you can run into problems. Run man cat to learn more about its options.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Alex Reynolds28k
0
gravatar for EagleEye
4.2 years ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:
If you wanted to be a bed file, try to make your 4th column as 5th ( the scores ) and you should have a name for each location as 4th column. Chr<tab>start<tab>end<tab>Peak1<tab>score Chr<tab>start<tab>end<tab>Peak2<tab>score Just follow this standard format, it should work. http://genome.ucsc.edu/FAQ/FAQformat.html#format1
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by EagleEye6.3k
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