How to download BED file with all the fields?
2
1
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12 months ago
kimkes25 ▴ 30

Hello,

my goal : to download a certain BED file from ucsc website that contains all these fields:

bin chrom   chromStart  chromEnd    name    score   strand  signalValue pValue  qValue  peak

I will describe my actions and my problem: - I go into the table browser(tools>Table Browser) and choose the parameters in the picture and the output file parameter as bed:

[1]

Capture1

[2]

Capture2

  • when I try to click " get output " I see this with a lot of fields missing as you can see:

[3]

Capture3

  • and when I go back to the table browser and now change the output format to "all fields from selected table" and get output I see in a new tab this:

[4]

Capture4

  • which is what I want but when I download there are 2 problems:
  • it I dont know if it is in BED format
  • the downloaded file looks like this :

[5]

Capture5

how can I get an output that looks like pic [4] with all of the required fields?

BED ucsc • 1.0k views
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0
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I meant when I download the file with output format "all fields from selected table" (with save as) I get this weird file:

downloaded outpu ( I got it by clicking save as from the tab that opened that is what I want)

output in new tb

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Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

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I fixed it now .can u take another look please?

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Output in image 3 is BED format (you will need to remove the track line at top). One in 4 with all fields no longer in BED format (BED format definition) but sounds like that is what you want.

Copy the contents (ctrl +a to select all text, ctrl +c to copy and then ctrv +v to paste into an editor and then save as "file.bed", replace ctrl with apple key if using macOS). I am not sure why you are not able to save the file as plain text out of the browser window.

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12 months ago
GenoMax 107k

If that information is not available then the fields are going to be missing. Not much you can do about that. Also don't go by visual inspection of the results in a browser. Tab delimited fields may not be displayed in columns that align if the contents of fields are different length. Using something like less -S file.bed should show the columns aligned properly.

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28 days ago
Luis Nassar ▴ 540

Hello,

If you would like to download the data the way it looks when all fields from selected table is selected, you need to add a name to the output filename: field which will prompt a download:

output filename in Table Browser

The reason the data looks different when you select BED output is because the Genome Browser is trying to conform the current format to BED. That track is in narrowPeak format (https://genome.ucsc.edu/FAQ/FAQformat.html#format12) which is a BED6+4, meaning the first 6 fields are standard BED fields (chrom, chromStart, chromEnd, name, score, strand) but then it has 4 additional fields. These additional fields are stripped to conform to BED output.

Another option is downloading the file directly from our download server: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/wgEncodeOpenChromDnaseHek293tPk.txt.gz

If you have any follow up questions, our public help desk can always be reached at genome@soe.ucsc.edu. You may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.

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+1 for goldenPath

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