Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Quality Control on Local Machine/Server

    Hello.

    I have done all the merging of the fastq files on the server, so all the files are on the server.

    However, my fastQC is installed locally. Is there a way to do QC on the server? or must I transfer all the files back locally to do QC?

    Thank you

  • #2
    FastQC will run fine on a unix server (long as java is available). You would need a X11 client on your local machine to project the GUI back to your desktop unless you have console access on the server.

    Comment


    • #3
      On a server, try something like:
      java -Xmx4g -jar Fastqc.jar *.fastq &

      Fastqc will analyse all fastq files in the directory and save the results.

      Comment


      • #4
        If you are not interested in running in interactive mode (GUI) then you can indeed use the command line as Colindaven pointed out.

        More information available here: http://www.bioinformatics.babraham.a...qc/INSTALL.txt Look for the section on "Running FastQC as part of a pipeline".

        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