Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SOLiD unmapped RNA-seq reads from TOPHAT

    Hello,

    I am working on SOLiD RNA-seq data. I would like to find chimeric transcripts or fusion genes discovery with this data. But, the softwares, which does fusion genes discovery were written for FASTQ format files.

    So, I tried converting my color space files to fastq by solid2fastq in BFAST and MAQ and the fusion genes discovery with the resulting files was a disaster as the conversion of .csfasta files to FASTQ is not straightforward as described in BFAST and MAQ

    I thought I can convert the mapped colorspace reads to FASTQ files and use those softwares.

    Is there a way to get the mapped reads and unmapped reads from TOPHAT? or any other alternatives to solve my problem?

    Any help in this regard will be greatly appreciated.

    Thanks,

  • #2
    A nice alternative might be to do mapping with eg bioscope in colourspace and then read the BAM files into R using a package like edgeR.

    I mention edgeR since they wrote a very nice step by step pdf, available on this forum, which could get you started.

    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
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X