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  • tophat error

    Hi,
    Am running tophat and this is the first time am seeing this error and I don't know how to correct it. Anyone out there with some ideas how to solve this.
    The error is:

    [Thu Feb 24 14:16:05 2011] Preparing output location SEQ1/
    [Thu Feb 24 14:16:05 2011] Checking for Bowtie index files
    [Thu Feb 24 14:16:05 2011] Checking for reference FASTA file
    [Thu Feb 24 14:16:05 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Thu Feb 24 14:16:05 2011] Checking for Samtools
    Samtools Version: 0.1.12a
    [Thu Feb 24 14:16:46 2011] Checking reads

    Error encountered parsing file /home/mh/Data/RNA_seq/110213_F/A_S.fq:
    Different read ID for sequence and quality (HWI-ST333_0073:2:1:1460:2172#ACCTGA/1 vs HWI-ST333_0073:2:1:1460:2172#gggggg/1)

    The code am using is:
    tophat -p 4 -o SEQ1 /home/mh/Data/RNA_seq/bowtie_indexes/mm9 /home/mh/Data/RNA_seq/110213_F/A_N.fq

    I have used this code before without any problems.

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