Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Table of transcript variant 1

    Hi all,
    I really hope that someone could help me.
    I would like to have a table that reports the information about the all the transcripts with the additional information of the number of the transcript variant (unfortunatelly refSeqGenes doesn't report this info).
    Just to give you an example I would like something like that

    A1CF NM_001198819.1 transcript variant 5
    A1CF NM_014576.3 transcript variant 1
    A1CF NM_138932.2 transcript variant 2
    A1CF NM_138933.2 transcript variant 3
    A1CF NM_001198818.1 transcript variant 4
    A1CF NM_001198820.1 transcript variant 6

    as it is reported in NCBI.
    Any suggestion?
    Really thanks in advance

  • #2
    Hi desmo,

    Download the following refseq file (~40Mb)

    ftp://ftp.ncbi.nlm.nih.gov/refseq/H_...man.rna.fna.gz

    unzip and use UNIX grep for the pattern A1CF

    Code:
    grep "A1CF" human.rna.fna
    output

    >gi|311771756|ref|NM_014576.3| Homo sapiens APOBEC1 complementation factor (A1CF), transcript variant 1, mRNA
    >gi|311771757|ref|NM_138932.2| Homo sapiens APOBEC1 complementation factor (A1CF), transcript variant 2, mRNA
    >gi|311771758|ref|NM_138933.2| Homo sapiens APOBEC1 complementation factor (A1CF), transcript variant 3, mRNA
    >gi|311771763|ref|NM_001198818.1| Homo sapiens APOBEC1 complementation factor (A1CF), transcript variant 4, mRNA
    >gi|311771765|ref|NM_001198819.1| Homo sapiens APOBEC1 complementation factor (A1CF), transcript variant 5, mRNA
    >gi|311771767|ref|NM_001198820.1| Homo sapiens APOBEC1 complementation factor (A1CF), transcript variant 6, mRNA

    To retrieve all IDs

    Code:
    grep "^>" human.rna.fna

    Comment


    • #3
      Really thanks rbagnall.
      It worked great.
      Thanks again

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 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