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Old 11-11-2014, 11:20 AM   #1
blcUT
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Default 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
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Old 11-11-2014, 01:20 PM   #2
Wallysb01
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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.
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Old 11-13-2014, 10:46 AM   #3
blcUT
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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
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Old 11-13-2014, 09:18 PM   #4
Wallysb01
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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
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assembly, chip seq, chrysalis, denovo, trinity

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