Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • The first step on RNA-Seq

    Hi All

    Hi I have got my raw data from biologist who running sequencing on Proton. I need to get the .fastq reads for downstreaming analysis (e.g. QC control, Alignment , DE analysis...) on Torrent Server by command line. I don't know that if Proton could output .fastq directly.

    I found that on Torrent Browser there is a panel called 'select a plugin to run'

    if I click 'FileExporter' ,there are 4 options

    Create SFF?

    Create FASTQ?

    Include Variant Caller Files (if available)?

    Zip results?


    If I select 2 and 4 and submit, there is not any response

    Btw, if I don't use Browser and use Torrent Server to run command line, how could I do it. I mean I don't know how to run FileExporter in Command line ,what is input and output?

    Thank you!


    Sorry this has been sorted cos is my plugin version's problem.
    Last edited by super0925; 03-14-2014, 06:54 AM.

  • #2
    The default output format for Ion Torrent is .bam (even if not mapping the reads).

    You need to fill out the settings for the FileExporter plugin before it will generate the .fastq files correctly.

    You will find the .bam files at:
    /results/analysis/output/Home/NAME_OF_RUN/

    and the .fastq files at:
    /results/analysis/output/Home/NAME_OF_RUN/plugin_out/downloads/

    (this is for the current version of TSS and may change with updates)

    Hope this helps.

    Comment


    • #3
      bamtools convert can convert bam to fastq

      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
      51 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