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  • beginning of quality values record not found & qual length () differs from seq length

    Hi all,
    i am using the newest version of tophat.
    Trying to align to Danio reiro Ensembl genome by using also gtf.
    We did RNAseq using HiSEQ2000.
    i am getting those errors as mention in the title....
    (each for diffrent run)
    Should i remove those reads?
    Or , there is other problem?

    My commandline is:
    /tophat-2.0.4.Linux_x86_64/tophat -r 430 -G /run/media/My\ Book/2la/reference/danRef7.gtf -p 8 -o /home/Desktop/tophat_iin /run/media/My\ Book/2la/reference/danRer7 /run/media/My\ Book/2la/RNAseq_zv9_All/Sample_ii-na_1.fastq /run/media/My\ Book/2la/RNAseq_zv9_All/Sample_ii-na_2.fastq

    Thanks,
    Pap

  • #2
    Have you tried checking your FASTQ files are valid? Perhaps one has been truncated or otherwise corrupted?

    Comment

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