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  • TopHat2 on multiple samples, avoid building Bowtie index from genes.fa each time?

    Hi all,

    Ultimately aiming at differential expression, I'm mapping human RNAseq read using tophat2 with the following command:
    Code:
    tophat2 --num-threads 12 --GTF /Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf /Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome myfastq_R1.fastq.gz myfastq_R2.fastq.gz
    Is it really necessary to:
    Code:
    [2014-09-18 10:38:45] Building transcriptome data files /tmp/genes
    [2014-09-18 10:39:21] Building Bowtie index from genes.fa
    Foreach sample? I mean - The different samples are all mapped using the same Bowtie2Index/genome files and the same Genes/genes.gtf files?

    Cheers,
    Leon

  • #2
    Have a look at the --transcriptome-index option, which is what you're looking for.

    Comment


    • #3
      Originally posted by dpryan View Post
      Have a look at the --transcriptome-index option, which is what you're looking for.
      Hi dpryan,

      Thanks for input reg. the --transcriptome-index option for tophat2. I looked it up in the TopHat2 manual. For other users, which may encounter the same challenge - The trick is to run this command first:
      Code:
      tophat2 -G iGenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf --transcriptome-index=transcriptome_data/known iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
      and then subsequently call tophat2 with this command:
      Code:
      tophat2 --num-threads 12 --transcriptome-index=transcriptome_data/known iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome myfastq_R1.fastq.gz myfastq_R2.fastq.gz
      After running the above command, you'll see
      Code:
      [2014-09-18 12:12:04] Using pre-built transcriptome data..
      Which is significantly faster, when running multiple samples.

      The UCSC/hg19 data can retrieved like so:
      Code:
      wget ftp://igenome:[email protected]/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
      Cheers,
      Leon

      Comment


      • #4
        tophat not creating transcriptome indexes

        Hi
        In my case The following command doesnt start tophat2. tophat2 just shows me the available options, like I have used a wrong option somewhere. Does anyone has an idea whats wrong here
        The command I use:
        tophat2 -G /home/chawla/rna_seq_pipeline/gff/mouse_ensembl.gff --transcriptome-index=tdata /home/chawla/rna_seq_pipeline/gff/mouse_ensembl

        Comment


        • #5
          Originally posted by konika View Post
          Hi
          In my case The following command doesnt start tophat2. tophat2 just shows me the available options, like I have used a wrong option somewhere. Does anyone has an idea whats wrong here
          The command I use:
          tophat2 -G /home/chawla/rna_seq_pipeline/gff/mouse_ensembl.gff --transcriptome-index=tdata /home/chawla/rna_seq_pipeline/gff/mouse_ensembl
          You have to point tophat2 process to the indexes for the full genome. It appears that you are including a gff file instead of the bowtie2 indexes at the end of your command. Refer to LeonDK's example in posts above.

          Comment


          • #6
            Thanks, it was actually old version of tophat that also needs an input read to create transcriptome indexes.

            Comment

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