Extending methylKit: Christmas Offer for Methylome Researchers

Next week is going to be a vacation and most of us are going on vacation. Me too. However, I thought that this Christmas I would OFFER fellow researchers a GOOD SERVICE. 

Many of the biologists are learning to deal with their high-throughput sequencing data. I also started just like you and spent hours and days learning R/Bioconductor related packages. Now, I thought I would SAVE your time and offer the data-analysis skills I have developed at most affordable price for the researchers (actually, my service is FREE, I collect charges only to PREVENT SPAM requests and some of it will go into developing further resources to help users like you)

Here are the details of my christmas offer: I am now offering methylation analysis for two samples (1 control and 1 test). As part of my offering you would get the following done:

• QC report of the FASTQ reads
• Mapping (hg19/mm10) using BISMARK
• Bisulfite efficiency analysis (if you have used lambda spike in)
• methylKit workflow to suit your needs
• Additional workflow in bioconductor to extract the list of genic elements/or non-genic elements with differentially methylated CpGs

Not only this, I also offer 30min - 1 hr consultation on planning methylome experiments (RRBS/WGBS). Yes, you read it right, I do data analysis and I build NGS libraries my self. So, I can help you planning experiments. I have built and sequenced over 100 RRBS libraries and 10 WGBS libraries from 10ng - 30ng DNA (I have NOT heard of any commercial service provider offering methylomes from such smaller amounts of DNA). So, with my tips you can build NGS libraries from very precious samples. I know the ins and outs of NGS library prep and good understanding of methylation analysis. I can see the QC and tell you what has gone wrong in the library prep (if there is any).

Price details:

1. RRBS/WGBS consultation (Sample processing, library prep, data analysis) for 30min to 1 hr : $15 for 30 min (total 6 slots for consultation)
2. RRBS data analysis as mentioned above : $ 50 (only 10 slots)
• I will also explain you the pipeline and the results will be delivered in neatly explained document/ppt. If necessary over skype/hangout
3. WGBS data analysis : $50 (only 1 slot)
• WGBS analysis will NOT cover the above data analysis due to huge cost of time and computational resources. I will do QC report, mapping and bisulfite efficiency analysis only.

Risk free:

1. After experiencing this service if you feel that my expertise is not useful for you, I WILL RETURN 80% of the price you PAID with NO QUESTIONS ASKED. All you have to do is just ask for your money. I am sure people reading this are true to their conscience. I do not want anybody to comment on this blog that they have lost money. So, my reputation is at stake if you are not satisfied.
2. If you happen to use the results, you need not give me any contribution. Its YOUR data. 

You can contact me using my personal email id at kalyankpy[at]gmail[dot]com for further details.

Disclaimer: Pls note that this is not marketing or business. I want to share my expertise and skill to the needed (I have been active in the methylkit_discussion forum on google groups for the topics I am familiar with). However, I don't want to invite SPAMMERS or JUNK. Price for this service is meant to invite genuine researchers only. Some of the money raised will be used in developing additional online resources for methylation anlaysis.

CpG Island shelves

Nowadays, regions with relatively lower CpG density are gaining importance in DNA methylation studies. This is based on the fact that a majority of CpG rich regions (CpG islands) are non-dynamic and less variant in terms of methylation status probed across a variety of tissues and cell populations (Irizarry 2009, Ziller 2013). It is now proven that methylation is more dynamic along the CpG shores (< 2kb flanking CpG Islands) and CpG shelves (<2kb flanking outwards from a CpG shore). While it is easy to retreive the genomic co-ordinates of CpG Islands from UCSC browser, public resources for retrieving the genomic co-ordinates for shores and shelfs were missing or scarce. Here, I am displaying the code (in R using Bioconductor package GenomicRanges) I use for generating objects for CpG islands, CpG island shores and CpG island shelves. The resulting objects are GRanges objects which could be used in multiple downstream applications in Bioconductor related packages.

Methylation Status of CpG Islands Across Human Genome

Researchers are aware that a majority of the CpG islands are unmethylated. How to represent this fact in a graphic? 

The above picture created with ggplot2 explains us how the CpG methylation across the CpG Islands is distributed for each chromosome. Each CpG island is shown as a single dot(.). Methylation on the CpG island is identified by the color gradient. This explains that most of the CpG Islands are unmethylated (overlapped dots are seen as a line on the left side of the picture). Sparsely methylated CpG Islands can be identified as blue dots on the right side. Click the picture for a larger view.