Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • looking for reference genome based assembler for short-reads

    Hi All,

    I want to use comparative-based assembler for short-reads for assembling mRNA-seq. For example, if we have human tissue mRNA short-reads, we want to reassemble the short-reads into transcripts by comparing with human genome, which software is more suitable for this task?

    I found AMOScmp-shortreads might be useful for this purpose, but when I read the manual, I found AMOScmp do not support fastq format. I also don't know the performance for this software.

    In further, do anyone compare the performance of de novo based assembler with reference-based assembler for mRNA-seq?

    Thanks,
    ZCH

  • #2
    The RNA-Seq section of the software wiki at this site has 14 entries; not all of them perform mapping but you should find several tools there which might be candidates for your needs.

    Comment


    • #3
      As the lists of this webpage "Software packages for next gen sequence analysis" includes many different tools for mapping/assembling. However, no any software designed for this purpose. MAQ has limited function to generate the consensus sequences based on mapping. However, it seems MAQ can only use reads length lower than 63bp. As I listed, AMOScmp-short-reads is only software I know to provide this function, but weak support for paired-end illumina GAII sequences files(qseq) or fastq.

      Comment


      • #4
        Check Tophat and Cufflink.
        Xi Wang

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X