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
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    Yesterday, 01:16 PM
  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 07:15 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 10:28 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 07:35 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Working...
X