Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Stats help, interpreting the output of bedtools fisher

    Forgive me if this is trivial, I want to make sure I understand the output of bedtools fisher. I've used it to compare several sets of intervals in the human genome and want to say whether two sets of intervals have a statistically significant overlap or not. Here are the abbreviated outputs from 6 tests (I can give the full outputs if needed):

    Code:
    Test   left    right   two-tail        ratio
    1:     0       1       0       3.655
    2:     1       1.3018e-39      2.5115e-39      1.180
    3:     1       4.9869e-47      9.3199e-47      1.198
    4:     1       3.7421e-45      6.909e-45       1.194
    5:     0.71641	0.40143	0.61502	1.123
    6:     0.63306	0.49828	0.86348	1.040
    Is it correct that: a small left p-value indicates the intervals overlap significantly more than expected (test #1 above), a small right p-value indicates the intervals overlap significantly less than expected (tests 2,3,4), and if neither the left or right p-values are small (tests 5,6) the intervals overlap "randomly" (not sure what the correct term is, basically they don't overlap more or less than would be expected)? Also I don't understand how to interpret the two-tail p-value and ratio for these tests. Thank you to anyone who can help clarify this for me.

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin


    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
    Yesterday, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
41 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
35 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
55 views
0 likes
Last Post seqadmin  
Working...
X