0
$\begingroup$

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.

$\endgroup$
1

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.