Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • pepeluisrr
    Junior Member
    • Jan 2017
    • 1

    #1

    bedtools intersect -f -F -r behavior

    Hello, I am using bedtools intersect and I'm failing to reproduce one of the examples in the documentation, bedtools intersect

    I am using bedtools v2.25.0

    In section "-r, and -f Requiring reciprocal minimal overlap fraction", the very simple example provided there is:
    $ cat A.bed
    chr1 100 200

    $ cat B.bed
    chr1 130 201
    chr1 130 200000

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -r -wa -wb
    chr1 100 200 chr1 130 201


    Well, in my case, when I try to force reciprocal overlap, the behavior is not what I expected. My output is:

    $ cat A.bed
    chr1 100 200

    $ cat B.bed
    chr1 130 201
    chr1 130 200000

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -wa -wb
    chr1 100 200 chr1 130 201
    chr1 100 200 chr1 130 200000

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -r -wa -wb
    chr1 100 200 chr1 130 201
    chr1 100 200 chr1 130 200000

    Last output is different from the example. -r seems to be ignored, I only get the expected reciprocal result manually using -F:

    $ bedtools intersect -a A.bed -b B.bed -f 0.50 -F 0.50 -wa -wb
    chr1 100 200 chr1 130 201

    Using -f and -r should be the same than using -f and -F, right?
    Does anyone have any idea of what I'm missing?

    Thank you so much for your feedback!

Latest Articles

Collapse

  • SEQadmin2
    Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
    by SEQadmin2



    CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

    Despite this, “CRISPR helped turn genome editing from a specialized technique into
    ...
    07-31-2026, 11:01 AM
  • SEQadmin2
    Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
    by SEQadmin2


    Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

    The systematic characterization of the human proteome has
    ...
    07-20-2026, 11:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 08-11-2026, 10:35 AM
0 responses
11 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 08-06-2026, 07:41 AM
0 responses
29 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 08-03-2026, 10:13 AM
0 responses
48 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 07-31-2026, 02:55 AM
0 responses
48 views
0 reactions
Last Post SEQadmin2  
Working...