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  • zhenbinhu
    Junior Member
    • Aug 2014
    • 4

    #1

    TASSEL command -FastqToTagCountPlugin

    Hi all,
    I running TASSEL3 for analysis the GBS data like following

    /.../tassel3_standalone/run_pipeline.pl -Xms1g -Xmx14g -fork1 -FastqToTagCountPlugin -i /.../fastq -k /.../GBS/GBSbarcodes.txt -e ApeKI -o /.../GBS/tagCounts -endPlugin -runfork1
    Memory Settings: -Xms1g -Xmx14g
    Tassel Pipeline Arguments: -fork1 -FastqToTagCountPlugin -i /.../fastq -k /.../GBSbarcodes.txt -e apeki -o /.../tagCounts -c 5 -endPlugin -runfork1
    [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.169 Date: July 24, 2014
    net.maizegenetics.gbs.pipeline.FastqToTagCountPlugin
    Using the following FASTQ files:
    /.../fastq/42A87AAXX_7_fastq.txt
    Reading FASTQ file: /.../fastq/42A87AAXX_7_fastq.txt
    Enzyme: ApeKI

    CTCC OWB003:42A87AAXX:7late1:A01
    ...
    CGCCTTAT OWBRec:42A87AAXX:7late1:H06
    Total barcodes found in lane:48
    Total barcodes found in lane:48

    But no any output.
    Thanks for your help.

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