Thanks Gjain !! :)
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Interpreting "Intersectbed" Output
Hello,
I have been trying to interpret the output produced by the "intersectBed" tool from the BEDTools suite. I could not find any documentation related to interpreting the output.
I used the basic command for intersectBed
ie. intersectBed -a file1.bed -b file2.bed
Here are some lines for the output :
chr8 579281 579420 . 375 . 4.88051 2.88614 2.16931 79
chr1 936133 936483 . 748 . 8.58236 15.39442 12.80621 181
While the first 3 columns describe the chromosome number, the start and the stop co-ordinates, I am unable to figure out what the rest of the numbers mean.
Any help on this would be much appreciated :)
Thank you.
AB
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Gjain
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Atom Smasher •
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1 answer
Hi Atom,
Its just the bed format. Main point here is that the start and end coordinates are the common(overlapped) coordinates for the two bed files.
So basically:
The first three required BED fields are:
- chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
- chromStart - The starting position of the feature in the chromosome or scaffold.
- chromEnd - The ending position of the feature in the chromosome or scaffold.
The 9 additional optional BED fields are:
- name - Defines the name of the BED line.
- score - A score between 0 and 1000.
- strand - Defines the strand - either '+' or '-'.
- thickStart - The starting position at which the feature is drawn thickly.
- thickEnd - The ending position at which the feature is drawn thickly.
- itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0).
- blockCount - The number of blocks (exons) in the BED line.
- blockSizes - A comma-separated list of the block sizes.
- blockStarts - A comma-separated list of block starts.
Example: Here's an example of an annotation track that uses a complete BED definition:
track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
For more details, please look at this link.
You can download the BEDTOOLs manual from this link.
I hope this helps.
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Cross-posted here.
What do file1.bed and file2.bed look like?
Hello Aaron, Both input bed files just have the chromosome number, start and stop co-ordinates. i.e
chr start stop
Hello Aaron, Both input bed files are just tab delimited files containing the chromosome number, start and stop coordinates.
try 'intersectBed -a file1.bed -b file2.bed -wa -wb'. It'll give you the overlapping entries of both files
Hello Aaron,
I'd like to know more about the score in the 5th column (ranging from 0 to 1000). Is that a score for the overlap between the two bed files ?
I intend to "rank order" the intersecting regions from the two bed files for my analysis to find out the regions with the most significant intersections.
Can I simply use the score to rank order the regions ? For instance, all the regions with a score of 1000 are more significant than those with a score less than 1000.