Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cuffdiff calculations

    Hi
    Everyone
    I have been trying to wrap my head around these problems and I am sorry if someone has posted these exact problems earlier:
    a) Does CUFFDIFF2 handles a .bam file that is a mixture of singletons and paired end fragments?
    I am little uncertain if it does that or not. Doesn't throw an error for sure.
    [Because the manual talks about fragments and how they are used to find assembled isoforms and then abundance estimation of the most likely isoforms, by that I mean most likely reads/fragments must have been generated from an isoform.]

    b) How does cuffdiff calculates (by that I mean the actual calculation not statistical explanation, just data, numbers and formula wise explanation) raw fragment counts, internally scaled and externally scaled counts in the files generated such as genes.count_tracking, isoform.count_tracking , genes.read_group_tracking, and isoform.read_group_tracking?

    c) In my experiment there 2 replicates for control and 2 for experiment. I used cuffdiff to find out the differentially expressed genes.
    I used -c 10 for my CUFFDIFF analysis.
    For a gene that has no isoform and is a single exon gene, I see a NOTEST when there is clearly enough reads in both of my experimental replicates(q1_exp=28,q2_exp=20).
    But when I check the genes.count_tracking=> 8.9382, and the raw fragment counts for q1_exp=15 and q2_exp=2,
    internal_scaled_frags external_scaled_frags
    q1_exp=> 15.8613 15.8613
    q2_exp=> 2.01515 2.01515

    This is a small genome and around 95% of genes in the GTF file do not have any isoforms, so I don't think there is any isoform switching going on over here.
    I just want to know how these numbers come from because the raw counts are different from my read count that involves the following strategy:
    samtools view *.bam scaffold_3:236757-237675 |cut -f1|sort|uniq -c |wc -l

    Hope this makes sense. Please help.
    I will be very grateful for your concern.
    Last edited by mparida85; 01-26-2014, 08:06 AM.

Latest Articles

Collapse

  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM
  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-28-2024, 06:12 AM
0 responses
27 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-23-2024, 04:11 PM
0 responses
74 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
82 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X