Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Extracting fastq from Illumina/Eland export?

    Hi,
    I was provided with some sequencing data that I want to run through my pipeline, and although my pipeline uses fastq, the data is in Illumina/Eland Export format.

    Any tips on how to covert such data to fastq? I am not even sure what some of the fields are

    Here is the first line:
    ILLUMINA-8879DC 215 1 1 18423 1029 0 1 NNNNNCAGANANNNANNNNNNGNNNNNNNNAAANA BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB QC

    N


    thanks for the help

  • #2
    Same Issue

    I'm working on the same issue. The _export format is specified in the CASAVA user guide.

    Is your data set paired? If not, there is a script fq_all2std.pl that is part of the maq project. Still _export files were intended to be an internal format.

    If your reads are from a paired-end analysis, then I think your issues are a bit more complicated. I have sets of paired reads (e.g. s_6_1-PGDX_export.txt and s_6_2-PGDX_export.txt) and I'm having a rough time getting them into fastq format that I can make use of and align to hg19 using bwa.

    If I sort it out, I'll post my solution.

    Comment


    • #3
      _export to fastq solution

      I got the _export.txt files from paired end reads to fastq files using GNU sort and a python script.

      Most of the procedure is detailed in a post over at Biostars.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Best Practices for Single-Cell Sequencing Analysis
        by seqadmin



        While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
        06-06-2024, 07:15 AM
      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        05-24-2024, 01:16 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:54 AM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-14-2024, 07:24 AM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-13-2024, 08:58 AM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-12-2024, 02:20 PM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Working...
      X