Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • xunong
    Junior Member
    • Sep 2014
    • 9
    #1

    identify single exon transcripts from cufflinks output

    Hey guys,

    Do you have an idea how to identify single exon transcripts from cufflinks output? Dose 'genes with only one exon' means exon_number "1" are eligible?
    The transcripts.gtf file looks like:
    chr1 Cufflinks transcript 11387 11823 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "126581774.1320091337"; frac "1.000000"; conf_lo "23084341.949073"; conf_hi "230079206.314945"; cov "2.510922"; full_read_support "yes";
    chr1 Cufflinks exon 11387 11823 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "126581774.1320091337"; frac "1.000000"; conf_lo "23084341.949073"; conf_hi "230079206.314945"; cov "2.510922";
    chr1 Cufflinks transcript 11874 29043 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528"; full_read_support "no";
    chr1 Cufflinks exon 11874 12227 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "1"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528";
    chr1 Cufflinks exon 12613 12721 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "2"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528";
    chr1 Cufflinks exon 13221 29043 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "3"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528";
    chr1 Cufflinks transcript 11874 14408 1 + . gene_id "CUFF.2"; transcript_id "NR_046018_1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "6894923.389408"; cov "0.000000"; full_read_support "no";
    Tags: None
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478
    #2
    Something like the following should work:
    Code:
    grep exon transcripts.gtf | awk '{print $10}' | sort | uniq -u
    The will likely give the list of single-exon genes, assuming cufflinks is consistent in its file formatting.

    Edit: I just saw that you wanted single-exon transcripts, not genes. Just change "print $10" to "print $12".

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • GATTACAT
      Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by GATTACAT
      Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
      Yesterday, 11:43 AM
    • SEQadmin2
      Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by SEQadmin2


      I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

      Here are nine questions we think about, in roughly the order they matter, before...
      06-18-2026, 07:11 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
    Started by SEQadmin2, Today, 11:08 AM
    0 responses
    6 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Today, 11:08 AM  
    New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2
    Started by SEQadmin2, 06-30-2026, 05:37 AM
    0 responses
    11 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-30-2026, 05:37 AM  
    Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2
    Started by SEQadmin2, 06-26-2026, 11:10 AM
    0 responses
    19 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-26-2026, 11:10 AM  
    Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
    Started by SEQadmin2, 06-17-2026, 06:09 AM
    0 responses
    53 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-17-2026, 06:09 AM  
    View All
    Working...