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  • Trimmomatic help

    Hello,

    I am trying to trim low quality bases from a .fq archive using Trimmomatic but I get the following error:

    Comand:
    Code:
    java -jar trimmomatic-0.36.jar SE -phred33 ORD0908_Forward.fq try.fq LEADING:3 TRAILING:3
    Output:
    Code:
    TrimmomaticSE: Started with arguments:
     -phred33 ORD.fq try.fq LEADING:3 TRAILING:3
    Automatically using 2 threads
    Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: >ORD
    	at org.usadellab.trimmomatic.fastq.FastqParser.parseOne(FastqParser.java:68)
    	at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:164)
    	at org.usadellab.trimmomatic.TrimmomaticSE.process(TrimmomaticSE.java:197)
    	at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:306)
    	at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)
    marta@martapc:~/Trimmomatic-0.36$
    It seems there's something wrong with first line..

    Thank you for helping
    Last edited by Neuls; 11-20-2016, 01:37 PM.

  • #2
    Looks like you're trying to trim a FASTA file (with sequence names starting with >), instead of a FASTQ file (with sequence names starting with @, and 4 lines per sequence): https://en.wikipedia.org/wiki/FASTQ_format

    Comment

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