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  • TopHat2 Error running 'prep_reads'

    Hi!
    I got this error when tried to run tophat2 with paired-end reads (150 in length): "Error: qual length (196) differs from seq length (150) for fastq record !"

    I checked the first pair of reads in the .fq files (_1 and _2) and both "qual length" and " seq length" have 150 characters. Guys, do you have any idea what is wrong???

    Also, is there some way to check for "integrity" of my .fq files? I obtained these files from one single file (unmapped.bam) with 1/2 paired reads of a previous successful tophat2 alignment. I don't know if some reads were affected after some commands to split and ordering the files.

    Thanks,

    Sandra

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