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  • Bowtie alignment with 0 mismatches

    Dear all

    I would like to align filtered and trimmed RNAseq reads to a reference genome. The reads are between 20-24 nt in lenght.
    I am using bowtie-1.2.2.
    ,
    First I made an reference index, and six reference index files were created. bowtie3.rev.1.ebwt, bowtie3.rev.2.ebwt, bowtie3.1.ebwt, bowtie3.2.ebwt. bowtie3.3.ebwt, bowtie3.4.ebwt.
    I then run the command from the directory where the reference files from the indexing are located:

    cd $PBS_O_WORKDIR
    module load bowtie-1.2.2

    bowtie -v 0 -x /nlustre/users/motto/TF/bowtie3 -q /nlustre/users/motto/TF/AFI-1_S1out.fastq.gz -S /nlustre/users/motto/TF/AFI-1_S1out2.sam

    But then continue to get the following error message:

    Could not locate a Bowtie index corresponding to basename "/nlustre/users/motto/TF/bowtie3"
    Command: /apps/bowtie-1.2.2/bowtie-align-l --wrapper basic-0 -v 0 -q -S /nlustre/users/motto/TF/margot /nlustre/users/motto/TF/AFI-1_S1out.fastq.gz /nlustre/users/motto/TF/AFI-1_S1out2.sam

    It can not find the reference index....can someone please advise?

    Kind regards
    Margot





  • #2
    I'm not sure. Maybe this old thread will help. https://www.biostars.org/p/372511/

    Comment

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