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  • How filter bcl2fastq reads ?

    Hello everyone,

    I got a nextseq run that I demultiplexed using bcl2fastq.
    Then I used fastq illumina filter and I got this strange result :

    fastq_illumina_filter (--keep N) statistics:
    Input: 141,900,316 reads
    Output: 141,900,316 reads (9%)
    According to the website where I've downloaded this software :
    This program can filter FASTQ files produced by CASAVA 1.8
    Indeed, all my reads (the 4 lanes) have the "N" tag I checked with the following command
    grep -A 3 '^@.* [^:]*:Y:[^:]*:'
    Why all my reads have the "N" tag ? According to the bcl2fastq user guide this tag DOES exist with bcl2fastq ! (page 22) So, is there a way to filter reads which are produced with bcl2fastq ? Do I have to update the RTA version ? And finally why fastq_illumina_filter gave me 9% of read passing filter ?

  • #2
    Forgive me if I am not understanding your question.

    Only way to get "failed" reads in output file is to run bcl2fastq with the option "--with-failed-reads".

    By default N stands for NOT filtered i.e. of good quality.

    Comment


    • #3
      Originally posted by GenoMax View Post
      Only way to get "failed" reads in output file is to run bcl2fastq with the option "--with-failed-reads".
      That's why I wasn't able to see them, thanks

      Comment

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