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
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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