Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • repinementer
    replied
    Yes you are right. There are no negative values. The least i observed was 0. And the library was rRNA depleted one.
    May I know the usual range of FPKM values people get ? And also where could I get the below mask.gtf file (Annotated rRNA and mitochondrial transcripts?)
    I will run again cufflinks by using -M mask.gtf file and will let you know.
    Last edited by repinementer; 11-18-2010, 10:55 PM.

    Leave a comment:


  • GKM
    replied
    There is no way you could get negative FPKMs.

    My suspicion is that the 444467 is either mitochondrial or ribosomal, or something of that sort, and the library may not even be polyA selected, but some sort of Ribo-depleted.

    If you provide these details, it would be helpful

    Anway, you may want to mask those regions when you run cufflinks, as they affect quantification of everything else, and if they aren't uniform across samples, they will affect any between-samples comparisons too.

    Leave a comment:


  • repinementer
    started a topic FPKM minimum and maximum values ?

    FPKM minimum and maximum values ?

    I successfully ran cufflinks and my gene.expr and transcripts.gtf and others are showing FPKM values. Maximum I observed in my data is 444467 FPKM and minimum is <0.

    Are my values are in correct range ?

    Cufflinks paper results figure show FPKM ranges from 10 -100.

    ANy suggestions ?

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
141 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
116 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
109 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X