Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Fastxtoolkit nucleotide distribution issue

    Hi all,
    I need some help on fastx-toolkit use.
    I would like to generate nucleotide distribution line graph but I don't manage.
    Below is command lines that I used :
    1-to obtain statistics report
    cat ../../sequences/phix/s_4_1_sequence.txt | fastx_quality_stats -o ../../sequences/phix/s_4_1_qual_stat.txt

    2-to create distribution graph
    fastx_nucleotide_distribution_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_s_4_1.png

    that worked.

    3-to create distribution line graph
    fastx_nucleotide_distribution_line_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_line_s_4_1.png

    It returned:
    Error: Input file is not a valid statistics report.
    This tool (fastq-quality-plot) requires a tabular text file conaining summary statistic about your FASTQ file.
    In Galaxy,
    Please use the "Compute Quality Statistics" tool (in the "NGS: QC and Manipulation" category) to compute the quality statistics report, and then use this tool with the new statistics report.
    On the command line,
    Please use the "fastx_quality_stats" program to create the statistics report.

    I thought both distribution scripts work similary and have only different output graphs. Maybe I am wrong.
    Why does it work in one case and not in the other with same statistics report file as input ?

    Thanks for help.
    Jennifer

  • #2
    Fastxtoolkit nucleotide distribution issue

    Hi,

    I don't know if it is correct, but I just commented out the lines of the file check from the shell file and it works without any problem.

    Good luck!
    Tirza
    --
    Tirza Doniger, Ph.D.
    Bioinformatics Unit
    The Mina and Everard Faculty of Life Sciences
    Bar Ilan University

    Comment


    • #3
      Hi Tirza,

      I commented lines that you suggested and it works.

      Many thanks,
      Jennifer

      Comment


      • #4
        encountering the same problem

        Please help me too...as I am encountering the same problem while using fastq quality box plot.sh
        This tool (fastq-quality-plot) requires a tabular text file conaining summary statistic about your FASTQ file.

        Comment


        • #5
          Hi,

          You don't have to comment it. In line 121 make this change:

          AWK_VALID_STAT='NR==1 && $1=="column" && $2=="count" && $3=="min" { exit 2 } NR>1 { exit}'

          The problem is that they put "cycle" instead of "column" which is the right header for the qual stats file.

          Cheers.

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