Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Gene ID in cuffmerge

    Hi everyone
    I have a question on IDs in cuffmerge output. I am doing cufflinks with -g annotation.gtf file. gene_id and transcript_id seem correspond to the gtf file.

    2L Cufflinks exon 7529 8116 1 + . gene_id "FBgn0031208"; transcript_id "FBtr0300689"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.001241"; cov "0.000000";
    2L Cufflinks exon 8193 9484 1 + . gene_id "FBgn0031208"; transcript_id "FBtr0300689"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.001241"; cov "0.000000";

    But to run cuffdiff I run cuffmerge first. Then the ids are changed to cufflinks id, which looks like (although I still used the -g option):
    2L Cufflinks exon 7529 8116 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "CG11023"; oId "FBtr0300690"; nearest_ref "FBtr0300690"; class_code "="; tss_id "TSS1"; p_id "P1";
    2L Cufflinks exon 8193 8589 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "CG11023"; oId "FBtr0300690"; nearest_ref "FBtr0300690"; class_code "="; tss_id "TSS1"; p_id "P1";

    As result when I used this merged gtf file to run cuffdiff, ids still remain in this format...

    I am running everything with annotation gtf file when -g option is available so I am not sure why this is still happening.
    Thanks for help in advance.

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:47 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Working...
X