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  • DeNovo ChIPseq and Trinity

    Hi all,

    I'm trying to assemble some ChIPseq for RNAPolII data in eukaryotes de novo, and I'm using Trinity as per the post doc in the lab's directions. Trinity is taking a monumental amount of time to complete the chrysalis step on our computing cluster, even though the data set is ~1/2 the size of RNAseq sets I've previously assemble de novo using trinity that took under 24 hrs to complete. Is trinity simply not appropriate for processing ChIP seq data? Has anyone else had success using Trinity for ChIPseq data? If this is a fool's errand, what other software might I use?

    Thanks

  • #2
    I’m not sure why you’d want to use trinity, since its set up to try to find splice forms. You could just use the inchworm assembly though I suppose.

    I’ve played around with de novo ChIPseq and found ABySS to work very well.

    Comment


    • #3
      What functionality do you use of ABySS?

      abyss-pe uses the following programs, which must be found in your PATH:

      ABYSS: de Bruijn graph assembler
      ABYSS-P: parallel (MPI) de Bruijn graph assembler
      AdjList: find overlapping sequences
      DistanceEst: estimate the distance between sequences
      MergeContigs: merge sequences
      MergePaths: merge overlapping paths
      Overlap: find overlapping sequences using paired-end reads
      PathConsensus: find a consensus sequence of ambiguous paths
      PathOverlap: find overlapping paths
      PopBubbles: remove bubbles from the sequence overlap graph
      SimpleGraph: find paths through the overlap graph
      abyss-fac: calculate assembly contiguity statistics
      abyss-filtergraph: remove shim contigs from the overlap graph
      abyss-fixmate: fill the paired-end fields of SAM alignments
      abyss-map: map reads to a reference sequence
      abyss-scaffold: scaffold contigs using distance estimates
      abyss-todot: convert graph formats and merge graphs

      Comment


      • #4
        use abyss-pe, but only in single end mode, i.e.:

        Code:
        $ABYSS_DIR/abyss-pe n=5 k=21 name=K27ac np=12 s=50 se='K27ac_rep1.fastq K27ac_rep2.fastq' > out.txt

        Comment

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