Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Sanger FASTQ Quality Scores

    Here is a Sanger FASTQ :
    @SRR034462.9 VAB_0176_20090326_2_WT_deg_10pskmusc_461_18_311_F3 length=35
    TGAGGGGTGGGGGGGTTTTTTTTTTTTTTTTTTTT
    +SRR034462.9 VAB_0176_20090326_2_WT_deg_10pskmusc_461_18_311_F3 length=35
    '4<),/;//40-8<'%2+)'((37+0,4+2.4<0:

    first i convert SOLID2Sanger ,but when i handle the sangerfastq,I don't know how to convert the fourth line that the quility line;how to convert it to decimal system.preferably be perl script;
    Thanks a lot!

  • #2
    Code:
    echo "'4<),/;//40-8<'%2+)'((37+0,4+2.4<0:" | 
    perl -e 'while(<STDIN>){chomp;@t=split("",$_);$qual.=((ord($_)-33)." ") for (@t);}print $qual;'
    
    6 19 27 8 11 14 26 14 14 19 15 12 23 27 6 4 17 10 8 6 7 7 18 22 10 15 11 19 10 17 13 19 27 15 25
    --
    Jeremy Leipzig
    Bioinformatics Programmer
    --
    My blog
    Twitter

    Comment


    • #3
      Originally posted by Zigster View Post
      Code:
      echo "'4<),/;//40-8<'%2+)'((37+0,4+2.4<0:" | 
      perl -e 'while(<STDIN>){chomp;@t=split("",$_);$qual.=((ord($_)-33)." ") for (@t);}print $qual;'
      
      6 19 27 8 11 14 26 14 14 19 15 12 23 27 6 4 17 10 8 6 7 7 18 22 10 15 11 19 10 17 13 19 27 15 25
      Zigster,
      thank you very much!I fix it use your script!
      Thanks!
      upper

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Recent Advances in Sequencing Technologies
        by seqadmin







        Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

        Long-Read Sequencing
        Long-read sequencing has...
        12-02-2024, 01:49 PM
      • seqadmin
        Genetic Variation in Immunogenetics and Antibody Diversity
        by seqadmin



        The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
        11-06-2024, 07:24 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 12-02-2024, 09:29 AM
      0 responses
      149 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 12-02-2024, 09:06 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 12-02-2024, 08:03 AM
      0 responses
      42 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 11-22-2024, 07:36 AM
      0 responses
      73 views
      0 likes
      Last Post seqadmin  
      Working...
      X