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  • Tophat2 can't find Bowtie index files *.ebwt

    I have run tophat2 using cmd:
    tophat2 --bowtie1 -p 6 -G /project/Ref_Genome/GRCm38.gtf -N 2 -r 40 --library-type fr-unstranded -o ./ /project/Ref_Genome/GRCm38.genome.fa /project/rawdata/mouse-1.fq /project/rawdata/mouse-2.fq
    but the following error occurs:
    Error: Could not find Bowtie index files /project/Ref_Genome/GRCm38.genome.fa.*.ebwt)
    I have checked that /project/Ref_Genome/GRCm38.genome.fa.*.ebwtl is produced.

    My software infomation is here:
    bowtie version 1.1.1
    TopHat v2.0.13

    Any suggestion?
    Thanks a lot!
    happy

  • #2
    This might be fixed in a more recent version. Not all of the versions have properly supported large indices for both bowtie1 and bowtie2.

    Comment


    • #3
      Thanks a lot @dpryan!
      I will have a try using bowtie2.
      happy

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