Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #46
    guys, now i am working on earthworm RNA sequencing. i need to study the gene expression of earthworm RNA seq.

    for gene expression analysis i use tophat and cufflinks.

    (ref: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks)

    i am already install all the software (tophat, cufflinks, bowtie, CummeRbund). for running these software i need reference genome.

    in that above ref. paper reference genome download via their website. but i am not able to download the reference genome. they ask username and password.

    so kindly help me to download the reference genome.

    then also help me to choose the reference genome which one is suitable for earthworm.

    Comment


    • #47
      Originally posted by dinesh21.ksd View Post
      guys, now i am working on earthworm RNA sequencing. i need to study the gene expression of earthworm RNA seq.

      for gene expression analysis i use tophat and cufflinks.

      (ref: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks)

      i am already install all the software (tophat, cufflinks, bowtie, CummeRbund). for running these software i need reference genome.

      in that above ref. paper reference genome download via their website. but i am not able to download the reference genome. they ask username and password.

      so kindly help me to download the reference genome.

      then also help me to choose the reference genome which one is suitable for earthworm.
      I find I can download the pre-built indexes without being asked for a username or password, from either the Bowtie, Bowtie2, or Illumina iGenomes web pages, links given below.







      You can always build your own index.

      I think your problem is going to be that the only worm reference genome on these web sites is C. elegans, which is probably not closely enough related to
      whichever earthworm species you are working with.

      If you can't find a closely-related reference genome, you can always try de novo transcriptome assembly.

      Comment


      • #48
        Originally posted by dinesh21.ksd View Post
        guys, now i am working on earthworm RNA sequencing. i need to study the gene expression of earthworm RNA seq.

        for gene expression analysis i use tophat and cufflinks.

        (ref: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks)

        i am already install all the software (tophat, cufflinks, bowtie, CummeRbund). for running these software i need reference genome.

        in that above ref. paper reference genome download via their website. but i am not able to download the reference genome. they ask username and password.

        so kindly help me to download the reference genome.

        then also help me to choose the reference genome which one is suitable for earthworm.
        Dinesh: First a suggestion. Start a new post for a question that is not directly related to a thread even if the title of the thread appears to be similar to what you are asking.

        You are the earthworm expert (relatively speaking) so you need to include additional information about which earthworm species are you specifically looking at/for.

        Here is an example earthworm genome that may or may not work for you.



        If the genome you are looking for is not available publicly (e.g. Amynthas) then you may need to assemble a transcriptome yourself using RNAseq data.

        Comment


        • #49
          tnx for the reply. i try ur suggested website http://support.illumina.com/sequenci...e/igenome.html. but i cant download in our campus internet because of some security problem.

          i try to ask in my university and get a permission to download that file .

          once again thank u

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Quality Control Essentials for Next-Generation Sequencing Workflows
            by seqadmin




            Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

            Nucleic Acid Quality Control
            Preparing for NGS starts with isolating the...
            02-10-2025, 01:58 PM
          • seqadmin
            An Introduction to the Technologies Transforming Precision Medicine
            by seqadmin


            In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
            01-27-2025, 07:46 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-07-2025, 09:30 AM
          0 responses
          66 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-05-2025, 10:34 AM
          0 responses
          101 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-03-2025, 09:07 AM
          0 responses
          81 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 01-31-2025, 08:31 AM
          0 responses
          45 views
          0 likes
          Last Post seqadmin  
          Working...
          X