bedtools annotate

Question

[alexmondaini]

Sorry for the trivial question but I can't understand the numbers in the fraction of each feature in bedtools annotate. Example from website:

$ cat variants.bed
chr1 100  200   nasty 1  -
chr2 500  1000  ugly  2  +
chr3 1000 5000  big   3  -

$ cat genes.bed
chr1 150  200   geneA 1  +
chr1 175  250   geneB 2  +
chr3 0    10000 geneC 3  -

$ cat conserve.bed
chr1 0    10000 cons1 1  +
chr2 700  10000 cons2 2  -
chr3 4000 10000 cons3 3  +

$ cat known_var.bed
chr1 0    120   known1   -
chr1 150  160   known2   -
chr2 0    10000 known3   +

$ bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed
chr1  100     200     nasty   1       -       0.500000        1.000000        0.300000
chr2  500     1000    ugly    2       +       0.000000        0.600000        1.000000
chr3  1000    5000    big     3       -       1.000000        0.250000        0.000000

Why the result on the first third column is 0.3 ?

chr1  100     200     nasty   1       -       0.500000        1.000000        0.300000

Is it 30 bases overlap divided by 100 ?

$ cat known_var.bed
chr1 0    120   known1   -
chr1 150  160   known2   -

/

  $ cat variants.bed
chr1 100  200   nasty 1  -

But then the 0.5 should be another value right ?

$ cat genes.bed
chr1 150  200   geneA 1  +
chr1 175  250   geneB 2  +

/

  $ cat variants.bed
    chr1 100  200   nasty 1  -

Should be 75/100 or .75.

[Pierre Lindenbaum]

cross posted: https://bioinformatics.stackexchange.com/questions/18012

Answer 1

[Istvan Albert]

It appears you need to compute the fractions only for intervals that are on the same strand.

[alexmondaini]

no I would just like to understand the output of this example.

[Istvan Albert]

It seems that you asked:

Why the result on the first third column is 0.3 ?

but you also answered it yourself.

you have it 20 bp from known1 + 10 bp from known2, 10+30=30 divided by 100 gives you 0.3

what is the question that you don't know the answer for?

[alexmondaini]

I think I got the point now. For the third column known1 + known2 add up to 30 . However the same does not apply for the first column first row result. The comparison would be the following:

chr1 100  200   nasty 1  -

with

chr1 150  200   geneA 1  +
chr1 175  250   geneB 2  +

Here we cannot just add 50 for geneA with 25 for geneB since the region 175-200 is covered both by geneA and geneB. On the other hand:

chr1 0    120   known1   -
chr1 150  160   known2   -

known1 and known2 are not overlapping regions, hence 30.

Right??