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  • 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

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