Cage peak bed file from bigbed

[Rhodes, Craig (NIH/NIDCR) [E]]

Hi UCSC genome browser,

 

I am trying to obtain a bed file, or file type more usable for the major  Cage peaks p1@gene from a bigbed  file http://fantom.gsc.riken.jp/5/datahub/mm9/peaks/mm9.cage_peak_phase1and2combined.bb

 

I am hoping the columns of the  cage peaks in this file will be p1@gene, chromosome coordinates, p2@gene chromosome coordinates etc.   The directions to convert bigbed to bed are at, supposedly.

 

http://hgdownload.soe.ucsc.edu/admin/exe/

https://genome.ucsc.edu/goldenpath/help/bigBed.html

 

I actually have no idea how to start to convert this file using this information. 

 

 

Here is the look at a gene with the major cage peaks shown, but I would like to use only one cage peak coordinate at the promoter, or so. 

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr13%3A89680241%2D89751437&hgsid=698199915_NnxR2AuaJSjAj6a6hooRLuW7jFac

 

Thanks so much for your time!

Craig Rhodes

[Jairo Navarro Gonzalez]

Hello Craig,

Thank you for using the UCSC Genome Browser and your inquiry.

Could you explain a bit more what you would like to achieve? As you are aware, you can convert the bigBed file to a BED file using the bigBedToBed tool. You can download the tool from our utilities directory for your operating system.

http://hgdownload.soe.ucsc.edu/admin/exe/

To convert the bigBed to a BED8 file, a BED file with the standard 8 columns, you can use the following commands:

bigBedToBed http://fantom.gsc.riken.jp/5/datahub/mm9/peaks/mm9.cage_peak_phase1and2combined.bb stdout | cut -f 1-8 > mm9.cage_peak_phase1and2combined.bed

An alternative to using the bigBedToBed tool is to use the Table Browser to get the BED coordinates. Using the Table Browser, you could choose fields you want, or you could do an intersection with a custom track. In the example you shared, the peaks are over the first exon, not upstream of it near the promoter or transcription start site (TSS). Unfortunately, if you want one peak per TSS, you will have to choose the best one. We don't offer a BED/custom track output option for upstream plus some bases after the txStart coordinate. However, if you just want the identifier and the chromosome coordinates, the Table Browser can give you those results.

You can follow these steps to get the identifier and chromosome coordinates using the Table Browser:

Step 1: Configure the Table Browser

With the FANTOM5 hub connected, apply the following settings.

clade: mammal
genome: Human
assembly: July 2007 (NCBI37/mm9)
group: Fantom 5
track: TSS peak
table: hub_21891_robustPeaks
region: genome
output format: BED - browser extensible data

Step 2: Get output

Once you have set the Table Browser settings, click get output.

You will be taken to a new page where you can create a BED record for each entry in the bigBed. Here is a sample of the output:

chr1    3309585    3309588    p@chr1:3309585..3309588,-    0    -    3309585    3309586
chr1    3367867    3367870    p@chr1:3367867..3367870,-    0    -    3367867    3367868
chr1    3479230    3479234    p@chr1:3479230..3479234,-    0    -    3479231    3479232
chr1    3644976    3644980    p@chr1:3644976..3644980,-    0    -    3644977    3644978
chr1    3657915    3657919    p@chr1:3657915..3657919,-    0    -    3657916    3657917
chr1    3661752    3661814    p1@Xkr4    0    -    3661803    3661804
chr1    3661851    3661889    p2@Xkr4    0    -    3661874    3661875
chr1    3664689    3664693    p@chr1:3664689..3664693,+    0    +    3664691    3664692
chr1    3863291    3863316    p@chr1:3863291..3863316,+    0    +    3863295    3863296

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genome Browser

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