Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Best reads normalization in RNA-Seq

    Hi, I'm analysing a bit of RNA-Seq data, in particular at the moment I try to compare the expression of genes in several conditions. To evaluate the expression value I used both FPKM value (Cufflinks v 1.3.0) and raw count (DESeq v 2.6). Due to the different number of reads of two samples (tipically about 10 million of reads!!), I suppose that I can't compare the value of a gene in this 2 samples; for example:

    FPKM_1=1 (or count_1=1) & FPKM=100 (or count_2=100) could not mean that there are differences between two condition (the difference is in order of size of one hundred).

    So, my question is: in the next step, do the software that perform differential analysis (like Cuffdiff or DESeq) allow for this difference?

    Otherwise, What's the best way to solve this problem?

    Thanks a lot.
    Mattia.
    Last edited by mattia; 04-17-2012, 05:50 AM.

Latest Articles

Collapse

  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    Today, 01:16 PM
  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 07:15 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 10:28 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 07:35 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Working...
X