Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cufflinks problem

    Hello,

    I tried to get gene expression level bby using tophat/cufflinks pipeline. I follow the step exactly like the flowchart in this link:


    I have no problem until step cuffquant and I get an error when I trried to do the cuffnorm step. The error said something about reconstituted expression bundle does not match GTF. I don't understand why this is happen. If there are anyboddy who has experience maybe you can share with me about this problem. And also, I'm quite confused about the GTF reference paraameter in each step. Which one we must used from UCSC/ensemble, which one we used from the transcript.gtf as a result of cufflinks, and which one we must use the merged gtf from cuffmerge. I will really appreciate for your experience sharing if you would because I'm really new to this tool.

    For me,
    cufflinks -> I use GTF from UCSC
    cuffmerge -> I still use GTF from UCSC
    cuffquant -> I use merged GTF from cuffmerge
    cuffnorm -> I use GTF from cuffmerge

    Thank you all.

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 on Modified Bases...
    Yesterday, 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, 04-11-2024, 12:08 PM
0 responses
40 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
41 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
36 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
55 views
0 likes
Last Post seqadmin  
Working...
X