Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Using tophat results via UCSC genome browser

    Hi all,

    Recently, I ran TopHat with 76bp reads data and got the results (sam, bed, and wig files).

    Actual a few lines of my input (fasta file) are:
    >HWUSI-EAS366:4:1:4:624#0/1:
    CTCNGGATGGAGTACAGTGGTGTGATCATGGCTCACTGTAGNNNNNANCNCNTGGGCGCAAGCNNNNNNNNNCTAN
    >HWUSI-EAS366:4:1:4:243#0/1:
    CGGNGCCGTTGCTGGTTCTCACACCTTTTAGGTCTGTTCTCNNNNNCNGNTNCGACTCTCTCTNNNNNANNNCCGN
    >HWUSI-EAS366:4:1:4:1373#0/1:
    GAAAAAACCACCCAGCGGTGATGGCAGCGCGCGTGGGTCCCNNNGNGNGNGGGGCGGGTCGCGCNNNNGNNNCGAN
    >HWUSI-EAS366:4:1:4:1672#0/1:
    GGGCAGGAAAAAAAGGGAAGANAAAATACTGGGGAAGAAAANNNANCNCNGTTTGGCAGCTCTTNNNNGNNNCAGN


    And a few lines of junctions.bed file are:

    track name=junctions description="TopHat junctions"
    gi|29823169|ref|NT_025004.13|Hs18_25160 9690 19656 JUNC00000001 1 + 9690 19656 255,0,0 2 37,38 0,9928
    gi|29823169|ref|NT_025004.13|Hs18_25160 14260 19654 JUNC00000002 2 + 14260 19654 255,0,0 2 57,36 0,5358
    gi|29823169|ref|NT_025004.13|Hs18_25160 19701 160104 JUNC00000003 3 + 19701 160104 255,0,0 2 32,66 0,140337


    A few lines of coverage.wig file are:

    track type=bedGraph name="TopHat - read coverage"
    gi|29823169|ref|NT_025004.13|Hs18_25160 0 9580 0
    gi|29823169|ref|NT_025004.13|Hs18_25160 9580 9655 1
    gi|29823169|ref|NT_025004.13|Hs18_25160 9655 9690 0


    Here is the problem.

    When I copied and pasted the results (either bed file or wig file), I always got an error and when I change the gi|29823169|ref|NT... part to something like chromosome name, it works.

    As you can see from my input file, I don't have gi|29823169|ref|NT... part. I am not sure where the TopHat find such label or reference.

    Can someone tell me what gi|29823169|ref|NT... part means and how I can convert these files into the one that UCSC genome brower understands. I think I need to get the actual chromosome names.

    Thank you,
    Statsteam

  • #2
    You might give Galaxy a try: http://main.g2.bx.psu.edu/

    On there you can upload the file and manipulate it into a format that you can use. I'm pretty new to bioinformatics so there might be a faster and easier way, but thus far it has been a very useful tool. Since you are wanting to upload the data to UCSC it would probably be best to place your data into a GFF file. I can give you a little walk through on using Galaxy to convert your BED file into a GFF.

    1. Go to http://main.g2.bx.psu.edu/
    2. Click 'Get Data' and then 'Upload File' select your file as a BED file and then browse for your file, select it, and then click Execute.
    3. Your data should be in separate columns automatically by selecting the file type as BED which should convert the pipes into tabs. From here it is just simple text manipulation.
    4. Click on 'Text Manipulation' and then you can manipulate your file by adding the necessary columns for the GFF format and then you can just simply cut them using the 'Cut' option to put them in order.

    Hope this helps.


    -Brandon

    Comment


    • #3
      Alternatively, you could download hg18/19 indexes from the Bowtie website and use them from now on (what you see now is a result of using the indexes built by NCBI assemblies), which use chromosome names consistent with the UCSC genome browser (chr1, chr2 etc), if you don't want to edit/run things yourself.

      Cheers,

      -- Leo

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X