Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Mothur and fastq file format

    Hi all.

    I am completly new at NGS. I have just got back my datas from a first run of 454 pyrosequencing. We want to get into metagenomics and we have decided to use mothur.
    Before to start with mothur, I'd like to have a look to my results using FastQC. The problem is that I don't have the fastq format, just the sff, fna and qual. I would know how to do that on linux, but we are using windows terminal. Does anybody now how to extract the file on windows? sff_extract doesn't work.

    By the way I would like to know which one would be the next step we must follow, I mean, from my demultiplexed samples. I guess it would be the denoising step, but not sure....

    Thanks for the help,

    Elisa

  • #2
    BBTools can change fasta+qual to fastq, and runs in Windows.

    Unzip and untar it (7-zip can do this) to some directory, for example C:\BBMap\

    Then you would run:

    java -ea -Xmx200m -cp C:\BBMap\current\ jgi.ReformatReads in=reads.fna qfin=reads.qual out=reads.fastq

    Let me know if you have any trouble!

    Comment


    • #3
      It didn't work
      I am working in the directory in which I have the files, and I get a message error saying :
      Exception in thread "main" java.lang.RuntimeException: can't find file 454Reads...then, there are more messages....

      Comment


      • #4
        Could you give the exact command line you used and the complete error message?

        Comment


        • #5
          One thing about FastQC is that it is geared towards analyzing high complexity sequences, so that that amplicons (I assume that's what you're doing) will likely cause warnings about overrepresented sequences. It will work ok for length, quality, etc. - though mothur also can tell you about those in a less fancy format.

          Comment


          • #6
            Originally posted by elizondas View Post
            Does anybody now how to extract the file on windows? sff_extract doesn't work.
            I am surprised, sff_extract is written in Python and so ought to work under Windows. Did you get an error message? What exactly was the command you ran?

            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
            7 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            7 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