Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How can I transfer txt file format NGS data

    I have dowloaded txt file NGS data from GEO, however the format of this file show like this:
    chr1:3053032-3053034 53 1 11.469303
    chr1:3333837-3333843 26 0 11.469303
    chr1:3334422-3334449 12 0 5.522257
    chr1:3473143-3473144 22 0 9.770147
    chr1:3671806-3671822 14 0 6.371835
    chr1:3937230-3937239 12 0 5.522257
    chr1:3985018-3985079 11 0 5.097468
    chr1:4141099-4141105 52 0 22.513818

    How can I transfer this to standard format like this
    #bin chrom chromStart chromEnd name score floatScore
    1470 chr7 116099071 116100373 26384 720 2.183
    1589 chr5 131622266 131623568 26442 679 2.06
    1590 chr5 131854028 131855330 26415 693 2.102
    1591 chr5 131859918 131861220 26451 675 2.048
    1592 chr5 132109996 132111298 26337 764 2.317
    1593 chr5 132140320 132141622 26374 729 2.21

    anyone can help?

  • #2
    Maybe you could give us some more information as to what your data is supposed to represent? If you got the data from GEO, then you should be able to find some documentation about it. Not knowing the format, my guess is:
    chr:start-end coverage ?? someScore

    I'll admit your "standard format" is a mystery to me. My guess is that it'll be impossible to do a 1-to-1 mapping, since your 2nd format has more information (bin number, name, 2 scores) than the first.

    You'll need to be more specific as to what you want to do, where your data comes if you want more substantial help.

    Comment


    • #3
      I just want to exchange ":" and "-" with TAB .
      I have solve this problem by transfer this data to Excell.Thanks!!

      Comment


      • #4
        With tr for example:
        tr :- '\t' < infile
        but in openoffice/libreoffice you can choose all the characters you want as field separators when loading external data and I believe that doing so is possible even on excel...

        Comment

        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...
          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
        55 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        52 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        45 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