Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cuffdiff output

    I am running BWA->cufflink for differential gene expression and the cuffdiff output contains many repeated gene_ids. For example:

    HTML Code:
    test_id	 gene_id	 gene	locus	sample_1 	 sample_2 	 status 	value_1	value_2	log2(fold_change)	 test_stat	 p_value	 q_value	 significant
    XLOC_000665	XLOC_000665	Traes_1AL_34404D5D8	IWGSC_CSS_1AL_scaff_3881073:2596-3747	q3	q5	OK	42.1649	2.81737	-3.90362	-8.49777	5.00E-05	0.00921445	yes
    XLOC_000665	XLOC_000665	Traes_1AL_34404D5D8	IWGSC_CSS_1AL_scaff_3881073:2596-3747	q4	q5	OK	16.8182	2.81737	-2.5776	-5.45754	0.00025	0.0386488	yes
    Can anyone explain why there are repeats like this?

    Also, I need to use BLAST against similar plant species to find information about the genes which are differentially expressed. I am not able to understand the "locus" column. In the above example, the locus is IWGSC_CSS_1AL_scaff_3881073:2596-3747. In the reference file there is a sequence associated with IWGSC_CSS_1AL_scaff_3881073. Do I need to select the subsequence starting from location 2596 to 3747 for BLAST?

  • #2
    Hi sbdk.

    Cuffdiff outputs a line for each ID, for each comparison.
    In the example you posted the first line is comparison between q3 and q5, and the second is between q4 and q5 for the same gene.
    Yu
    Yu

    Comment


    • #3
      Thanks Yu !!

      Actually I have two samples of data with three replicates in each sample. Thus I have 6 fasta files. So each data file represented by qi (i = 1,2 ..6) ? I used cufflink and then cuffmerge before using cuffdiff.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Quality Control Essentials for Next-Generation Sequencing Workflows
        by seqadmin




        Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

        Nucleic Acid Quality Control
        Preparing for NGS starts with isolating the...
        02-10-2025, 01:58 PM
      • seqadmin
        An Introduction to the Technologies Transforming Precision Medicine
        by seqadmin


        In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
        01-27-2025, 07:46 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 02-07-2025, 09:30 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-05-2025, 10:34 AM
      0 responses
      113 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-03-2025, 09:07 AM
      0 responses
      90 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 01-31-2025, 08:31 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Working...
      X