Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Assemble RNA-Seq reads

    Hi, everyone

    Recently, I wanted to find some software which can assemble the RNA-Seq reads into transcripts. I have tried Velvet and Cufflinks. But because velvet is mainly design to assemble DNA sequencing reads and maybe couldn't correctly assemble RNA-Seq reads. So I used Cufflinks to assemble the RNA-Seq reads finally. But I am confused that why the transcripts in Cufflinks outputs file only contain one start and one end coordinate on the genome? One transcript may contain several exons. Furthermore, Cufflinks can't output the transcript sequences. Can anyone recommend me some sotfware which can assemble RNA-Seq reads? Thanks.


    Sincerely,

    Geng

  • #2
    Oases: http://www.ebi.ac.uk/~zerbino/oases/

    Comment


    • #3
      Originally posted by chengeng View Post
      Hi, everyone

      Recently, I wanted to find some software which can assemble the RNA-Seq reads into transcripts. I have tried Velvet and Cufflinks. But because velvet is mainly design to assemble DNA sequencing reads and maybe couldn't correctly assemble RNA-Seq reads. So I used Cufflinks to assemble the RNA-Seq reads finally. But I am confused that why the transcripts in Cufflinks outputs file only contain one start and one end coordinate on the genome? One transcript may contain several exons. Furthermore, Cufflinks can't output the transcript sequences. Can anyone recommend me some sotfware which can assemble RNA-Seq reads? Thanks.


      Sincerely,

      Geng
      Geng:
      You should try aligning your reads using Tophat (since it also aligns reads spanning splice junctions). You should then use Cufflinks to assemble the Tophat SAM. If you only use bowtie or any other aligner that only maps reads within exons, then Cufflinks will not find any isoforms of transcripts.

      hope this helps
      Siva
      ps: When you deal with mRNA-seq reads you have enriched your sequence for spliced transcripts. So all reads falling within a spliced exon will be 'collapsed' into a transcript. If any one thinks I have got it wrong, please correct me.
      Last edited by Siva; 05-08-2010, 02:16 PM.

      Comment


      • #4
        Siva,

        Thank you very much for your help. I will try it again.

        Comment


        • #5
          Simon Anders,

          Thanks. But Oases paper hasn't published, we can't cite it.

          Comment


          • #6
            Help with assembling RNA-Seq reads.

            Hi all.

            I dont know is this the thread i should be subscribing. if not sorry. I have a small question. i have ran tophat and cufflinks on RNA-Seq data. I got the output .gtf file. Now i wanted to make a transcript fasta file. I dont know how can i do that.
            Please help.
            Thank you in advance.

            Deepak

            Comment


            • #7
              Originally posted by oxydeepu View Post
              Hi all.

              I dont know is this the thread i should be subscribing. if not sorry. I have a small question. i have ran tophat and cufflinks on RNA-Seq data. I got the output .gtf file. Now i wanted to make a transcript fasta file. I dont know how can i do that.
              Please help.
              Thank you in advance.

              Deepak
              Start a new thread please, with this same question. But to get you started, check out Scripture at http://www.broadinstitute.org/software/scripture/home

              Comment


              • #8
                Hi Robbe..

                I dont know how to start a new thread that is why i subscribed this post.
                Please suggest me how to..

                Thank you
                Deepak

                Comment


                • #9
                  Go here
                  Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


                  An then click on New Thread to the left.

                  Comment


                  • #10
                    Thank you.
                    I will create a new post.

                    Comment


                    • #11
                      Originally posted by chengeng View Post
                      Simon Anders,

                      Thanks. But Oases paper hasn't published, we can't cite it.
                      Oases has been published...



                      I use it quite a bit and find it to be very good.

                      Comment


                      • #12
                        Originally posted by jgibbons1 View Post
                        Oases has been published...



                        I use it quite a bit and find it to be very good.
                        Note the date that the comment you replied to was created and when the paper was submitted

                        Comment


                        • #13
                          Originally posted by dpryan View Post
                          Note the date that the comment you replied to was created and when the paper was submitted
                          Ahhh...you're right! Whoops...

                          Comment

                          Latest Articles

                          Collapse

                          • seqadmin
                            Genetic Variation in Immunogenetics and Antibody Diversity
                            by seqadmin



                            The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
                            11-06-2024, 07:24 PM
                          • seqadmin
                            Choosing Between NGS and qPCR
                            by seqadmin



                            Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
                            10-18-2024, 07:11 AM

                          ad_right_rmr

                          Collapse

                          News

                          Collapse

                          Topics Statistics Last Post
                          Started by seqadmin, Today, 06:13 AM
                          0 responses
                          9 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, 11-01-2024, 06:09 AM
                          0 responses
                          30 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, 10-30-2024, 05:31 AM
                          0 responses
                          21 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, 10-24-2024, 06:58 AM
                          0 responses
                          26 views
                          0 likes
                          Last Post seqadmin  
                          Working...
                          X