Thu, 12/12/2013
Customer says she is confused about analysis tools suitable for analyzing the MeDIP-seq she has got.
Thu, 12/12/2013 at 7:57 AM
Customer: My research area is DNA methylation. I tested the sheep methylome by MeDIP-seq. Each sample has 4G data. Now my question is which analysis method fits my data. some papers used MACs software to analyze DNA methylation data which suits ChIP-seq better. Others used Batman, MEDIPS and so on, but I found that those method are use Bayesian model, and need BS-seq reference, unfortunately, we do not have BS-seq yet.
Fri, 12/13/2013 at 11:40 AM
AccuraScience LB: Batman and MEDIPS were developed specifically for MeDIP-seq analysis, and should work fine without a BS-seq reference.
Sun, 12/15/2013 at 11:59 PM
Customer: I send you the MEDIPS tutorial of R . I tried to install it and run with it, but after I found it need BSgenome package, I stopped it…
Mon, 12/16/2013 at 11:38 A
AccuraScience LB: BSGenome stands for "Biostrings-based genome data", and it is a standard genome package in bioconductors. MEDIPS does not require BS-seq as reference.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer’s privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.