Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • rainmaker
    Junior Member
    • Jul 2013
    • 1
    #1

    Referance Genome - Noob Question

    Hello eveyone,

    I'm very new at this subject, and I need help about alingment of RNA-seq reeds. I want to make some trys on the data(>110GB) of this project. I downloaded Sequence Read Archive (SRA) from NCBI. How can I make an alignment on them. How can I use TopHat without refererance genome or how can I find reference genome of all primates which is used in this project.

    Or am I thinking very wrong by thinking to make DEseq on primates RNAseq data.

    If you know a tutorial page or video for this job please share with me.

    Please don't hurt me about my noob question, you can share with me other basic question forums.

    Thank you...
    Last edited by rainmaker; 07-06-2013, 07:10 AM.
    Tags: deseq, reference genome, rnaseq
  • mastal
    Senior Member
    • Mar 2009
    • 666
    #2
    Referance Genome - Noob Question

    The paper you mentioned has links to the software that they used for the analysis.

    You could try downloading and trying that software, or you could use the Trinity software, from the Broad Institute

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • GATTACAT
      Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by GATTACAT
      Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
      07-01-2026, 11:43 AM
    • SEQadmin2
      Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by SEQadmin2


      I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

      Here are nine questions we think about, in roughly the order they matter, before...
      06-18-2026, 07:11 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2
    Started by SEQadmin2, 07-02-2026, 11:08 AM
    0 responses
    21 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    07-02-2026, 11:08 AM  
    New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2
    Started by SEQadmin2, 06-30-2026, 05:37 AM
    0 responses
    22 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-30-2026, 05:37 AM  
    Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2
    Started by SEQadmin2, 06-26-2026, 11:10 AM
    0 responses
    21 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-26-2026, 11:10 AM  
    Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
    Started by SEQadmin2, 06-17-2026, 06:09 AM
    0 responses
    54 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-17-2026, 06:09 AM  
    View All
    Working...