Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to get target gene from BED format

    Recently I download the BED file from GEO, the authors used ChIP-Seq to find the ERa bing site genome-wide,but just supply the peak, the question is how to find the likely regulated target genes from these peaks?

    here is the format:

    Code:
    track name=ER_E2 description=ER_E2
    chr1	557112	558114
    chr1	559459	560286
    chr1	998864	999397
    chr1	999399	999604
    chr1	1004343	1005146
    chr1	1070346	1071080
    chr1	1305474	1306502
    chr1	1358287	1358744
    chr1	1776987	1777750
    chr1	1820476	1821168
    chr1	1922754	1923628
    chr1	2131962	2132747
    chr1	2325805	2326447
    chr1	2368996	2369977
    ....
    when I load all these data in UCSC,there is a error happend,and puzzled me.

    Could someone give me some clue convert these bing-sites to target genes?

    I know some R language but no idea completely.



    here is the website:ftp://ftp.ncbi.nih.gov/pub/geo/DATA/...2_peaks.bed.gz



    thx!

  • #2
    cisgenome has a bunch of useful executables (windows exe and LINUX binaries) and I suggest this one
    refgene_getnearestgene

    Comment


    • #3
      thank you for your reply very much,

      I used cisgenome for some time,
      when i used the tool to 'file format convert--> bed to cod',there is no result but just a flash of command line.I think there could be some problem come from the Bed file,which confuse me much.

      could somebody shed some light for me? thx very much

      Comment


      • #4
        Just ad a "rank#" column to the beginning and label the next columns "chromosome" "start" "end" If you do not have more than 1.05 Mio rows you can doe it easily in Excel.
        This is essentially a cod file format. good luck

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Quality Control Essentials for Next-Generation Sequencing Workflows
          by seqadmin




          Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

          Nucleic Acid Quality Control
          Preparing for NGS starts with isolating the...
          02-10-2025, 01:58 PM
        • seqadmin
          An Introduction to the Technologies Transforming Precision Medicine
          by seqadmin


          In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
          01-27-2025, 07:46 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-07-2025, 09:30 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-05-2025, 10:34 AM
        0 responses
        107 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-03-2025, 09:07 AM
        0 responses
        83 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 01-31-2025, 08:31 AM
        0 responses
        47 views
        0 likes
        Last Post seqadmin  
        Working...
        X