Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cuffmerge drops gene_ids and transcript features?

    Hello All,

    I have run cufflinks on 6 different samples. I want to use cuffmerge to combine the .gtf files for cuffdiff. However, I have two problems.

    ex. ind.gtf:
    GL349621.1 Cufflinks transcript 163188 166581 1000 - . gene_id "ACYPI52640"; transcript_id "ACYPI52640-RA"; FPKM "16.6471765920"; frac "0.641012"; conf_lo "15.699389"; conf_hi "17.594964"; cov "133.457105"; full_read_support "yes";
    GL349621.1 Cufflinks exon 163188 164381 1000 - . gene_id "ACYPI52640"; transcript_id "ACYPI52640-RA"; exon_number "1"; FPKM "16.6471765920"; frac "0.641012"; conf_lo "15.699389"; conf_hi "17.594964"; cov "133.457105";


    merged.gtf:
    GL349621.1 Cufflinks exon 159336 159819 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.3.1"; tss_id "TSS1";
    GL349621.1 Cufflinks exon 159902 160013 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; oId "CUFF.3.1"; tss_id "TSS1";


    1) In the third column of the ind.gtf files there are exons and transcript. When I run cuffmerge the transcript lines are not there? Only exon features are left.

    2) In the ind. gtf files I have gene_ids, but when my files are merged cuffmerge seems to remove the gene_id's and replace them with the XLOC numbers. Is there any way to prevent this from happening?

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
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
12 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
69 views
0 likes
Last Post seqadmin  
Working...
X