Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GKM
    replied
    Are you sure it is not predicting directionality for all the transcripts, i.e. you didn't look at the first X of them and got that impression? It will not give you directionality for transcripts that don't have introns, so if you had a lot of those in the beginning of your file, this could explain it.

    Leave a comment:


  • kmcarr
    replied
    Zorph,

    Cufflinks will impute strand (directionality) to the gene models it predicts based on the canonical directionality if splice junctions. If there are a sufficient number of junction crossing reads in a predicted gene model, cufflinks will assign a strand to that model. It does not require stranded reads to do this since it is the directionality of junction site which is important.

    As to why cufflinks is not predicting orientation for the models from your SOLiD data I can't say for sure. Perhaps there at not enough junction reads among your SOLiD data for cufflinks to predict orientation of the underlying gene model.

    Leave a comment:


  • zorph
    started a topic Cufflinks GA and Directionality

    Cufflinks GA and Directionality

    Hello,
    I was trying to compare RNA-seq samples run on the solid platform and the GA platform.
    I aligned my GA data on using Tophat.
    My Solid data was aligned using bioscope.

    Then both samples were analyzed using Cufflinks and Cuffcompare.

    My question is, on my .loci file, i have strandness information about my GA read that align to non-annotated areas. This should not be possible because my GA library was paired-end, hence no directionality.

    My Solid data on the other hand seems to be lacking a lot of strandness information. Edit: my Solid reads were adapted specifically to have directionality.

    Can anyone tell me what is going on? Thanks in advance.
    Last edited by zorph; 09-08-2010, 09:48 AM.

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, 07-16-2024, 05:49 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
31 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
40 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
205 views
0 likes
Last Post seqadmin  
Working...
X