Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • illumina to fastq

    I'm new to working with NGS and we have some illumina reads we'd like to convert to fastq.
    I've read the posts and tried to run the script qseq2fastq.pl on the samples w/o success.

    the files have the following format which doesn't look quite like qseq:

    USI-EAS39:1:1:2:1362#0/1:CTGGNTTCCACAGGCACATAGCCAAACCGGTGCCT:32 32 29 24 4 28 33 32 32 34 32 34 32 30 33 33 32 33 33 33 33 32 33 29 30 33 33 33 28 21 26 30 30 33 30

    Appreciate any conversions ideas.

    Charles

  • #2
    The script below should convert this format of data into a fastq file with Illlumina 1.5 quality encoding (you can change the offset value on line 20 if you'd prefer Sanger format).

    Code:
    #!/usr/bin/perl
    use warnings;
    use strict;
    
    my ($infile,$outfile) = @ARGV;
    
    die "Must specify input and output filename\n" unless ($outfile);
    
    open (IN,$infile) or die $!;
    open (OUT,'>',$outfile) or die $!;
    
    while (<IN>) {
      chomp;
      my @sections = split(/:/);
    
      my @qualities = split(/\s+/,$sections[-1]);
    
      my $quality_string = '';
    
      $quality_string .= chr($_ + 64) foreach (@qualities);
    
      my $seq_id = join(":",@sections[0..4]);
      print OUT '@',$seq_id,"\n",$sections[5],"\n+",$seq_id,"\n",$quality_string,"\n";
    
    }
    
    close OUT or die $!;

    Comment


    • #3
      Thanks Simon,

      what should the offset be for sanger fastq?

      Charles

      Comment


      • #4
        Originally posted by crh View Post
        what should the offset be for sanger fastq?
        33 (apparently I need to add some more text otherwise the forum won't allow the post...)

        Comment


        • #5
          Thanks again Simon - works fine.

          Is the original format I have 'Gerald'?

          Charles

          Comment


          • #6
            Biopython Seq I/O does these conversions. Pretty easy to use and with pretty good documentation.
            --------------
            Ethan

            Comment


            • #7
              Originally posted by crh View Post
              Thanks again Simon - works fine.

              Is the original format I have 'Gerald'?

              Charles
              It's a very old Solexa format called SCARF (Solexa Compact ASCII Read Format). It's not used anymore. Is this data really old?
              Last edited by kmcarr; 04-08-2011, 12:14 PM. Reason: Expand acronym

              Comment


              • #8
                I've used bioperl mostly, I'll check if they have seq conversions for illumina formats.
                regarding the reads, I believe they are ~2 yrs old now.

                thanks

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  Essential Discoveries and Tools in Epitranscriptomics
                  by seqadmin




                  The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
                  04-22-2024, 07:01 AM
                • seqadmin
                  Current Approaches to Protein Sequencing
                  by seqadmin


                  Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                  04-04-2024, 04:25 PM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Yesterday, 11:49 AM
                0 responses
                15 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-24-2024, 08:47 AM
                0 responses
                16 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-11-2024, 12:08 PM
                0 responses
                62 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 04-10-2024, 10:19 PM
                0 responses
                60 views
                0 likes
                Last Post seqadmin  
                Working...
                X