Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Annotate gene list

    I would like to annotate the results output file from Desq2 so it contains gene names and symbols. The RNA-seq count file I have used comes from Dexseq and contains ensembl gene IDs:
    ENSMUSG00000000001:001
    ENSMUSG00000000001:002
    ENSMUSG00000000001:003
    etc.
    These refer to the the different exons of the gene.
    I cannot annotate the result file because it contains the different exons. So how can I combine or merge the different exon counts for the same gene into one count for the gene?
    Thanks in advance

  • #2
    I am not sure I understand completely, but if you have a file

    Code:
    ENSMUSG00000000001:001
    ENSMUSG00000000001:002
    ENSMUSG00000000001:003
    ENSMUSG00000000002:001
    ENSMUSG00000000002:002
    ENSMUSG00000000002:002

    you could use:

    Code:
    awk -F':' -v OFS='\t' '{sum[$1]+=$2} END{for (key in sum) print key, sum[key]}' file.txt
    ENSMUSG00000000001      6
    ENSMUSG00000000002      5
    Hope this helps.
    Last edited by cmccabe; 09-11-2015, 06:10 AM. Reason: added awk

    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
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    50 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X