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
        Best Practices for Single-Cell Sequencing Analysis
        by seqadmin



        While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
        06-06-2024, 07:15 AM
      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 07:24 AM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 08:58 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-12-2024, 02:20 PM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-07-2024, 06:58 AM
      0 responses
      184 views
      0 likes
      Last Post seqadmin  
      Working...
      X