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  • Tophat with bowtie2

    Hi,

    I want to align the Rna-seq data using bowtie2.so here are the steps i did(i installed tophat,bowtie2 and samtools and kept in bashprofile)

    i got the reference genome from bowtie2(hg19) and i ran the makescript for indexing them.i got
    6 index files(hg19.1.bt2 hg19.2.bt2 hg19.3.bt2 hg19.4.bt2 hg19.rev.1.bt2 hg19.rev.2.bt2)and i kept in genome folder hg19

    now i want to run the tophat by takine these index files and the fastq file like this but i am getting error
    [ab RNASEQ]$ tophat /net/gs/vol3/shared/lab/RNASEQ/hg19/hg19 C_RNAseq_1.fq

    [Thu Nov 29 23:45:21 2012] Beginning TopHat run (v1.4.1)
    -----------------------------------------------
    [Thu Nov 29 23:45:21 2012] Preparing output location ./tophat_out/
    [Thu Nov 29 23:45:21 2012] Checking for Bowtie index files
    Error: Could not find Bowtie index files /net/gs/vol3/shared/lab/RNASEQ/hg19.*

    can anyone help me with this?i am new in using the tophat

    Thank you

  • #2
    It looks like tophat thinks that your index is in
    Code:
    /net/gs/vol3/shared/lab/RNASEQ/
    not
    Code:
    /net/gs/vol3/shared/lab/RNASEQ/hg19/
    . Try moving your index to a folder that does not include "hg19" in its name - it seems to be confusing tophat. Say
    Code:
    /net/gs/vol3/shared/lab/RNASEQ/my_index/
    should do the trick.

    EDIT: It looks like I did not notice the elephant in the room - you are using TopHat v1.4.1 which does not support Bowtie 2. Use Tophat version >2.0. From TopHat website:
    Version 2.0.0 is a major release adding Bowtie 2 support
    Last edited by mknut; 11-30-2012, 01:53 AM. Reason: misread the question

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    • #3
      [Thu Nov 29 23:45:21 2012] Beginning TopHat run (v1.4.1)
      You cannot run tophat 1.4 with Bowtie2. You have to install Tophat version 2.0.* if you want to use Bowtie2.

      kamal

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      • #4
        thank you

        Its working now

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