Tutorial: InsideDNA: Runinng Bismark pipeline for analysis of sodium bisulfite-treated DNA sequennces
gravatar for shilparaopradeep
3.1 years ago by
shilparaopradeep180 wrote:

BS-seq is an important method for analysis of DNA methylation. It provides a snapshot of a cell's epigenomic state and reveals genome-wide cytosine methylation at single base resolution. One of the powerful tools for BS-seq data analysis is Bismark suite. Bismark can discriminate between cytosines in CpG, CHG and CHH context and allow to visualize and interpret methylation data. Output data can be mapped to genome viewer. In this tutorial, we demonstrate basic usage of Bismark in InsideDNA platform.

Cytosine methylation of DNA is an epigenetic mechanism which plays an important role in control of gene expression, silencing or genomic imprinting. Next generation sequencing allows three different methods to study DNA methylation: methylated DNA immunoprecipitation (MeDIP-Seq) or methylated DNA binding domain sequencing (MBD-Seq) and direct sequencing of sodium bisulfite-treated DNA (BS-Seq). Bismark is a suite of seven tools for efficient analysis of BS-Seq sequences. Basic pipeline includes bismark_genome_preparation tool for preparation of reference genome; bismark tool for alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls; and bismark_methylation_extractor script which extracts the methylation call for every single C analysed.

In this tutorial, we will explain how to use Bismark within InsideDNA both through the UI interface and console. You can download entire dataset for this tutorial here or by clicking on Download data button at the top of the page. Read more:


ADD COMMENTlink modified 3.1 years ago by Istvan Albert ♦♦ 80k • written 3.1 years ago by shilparaopradeep180

You might want to mention in the title/tags that this is using some sort of web-based front end.

ADD REPLYlink written 3.1 years ago by Devon Ryan89k

Yes, I think you should add the word InsideDNA to the title (and tags) to indicate both that the tutorial is not hosted here but at another site (I actually just did this for you). It is fine to link to tutorials, but let's help people understand that.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Istvan Albert ♦♦ 80k

All the posts from the OP are created in a similar fashion. Either someone edits all the posts or suspend the user?

ADD REPLYlink written 2.8 years ago by Sukhdeep Singh9.7k

I've added "InsideDNA" to the title so at least now people at least have a clue that these have something to do with their platform. I guess they should all be tagged appropriately too, though I haven't yet bothered to do that.

ADD REPLYlink written 2.8 years ago by Devon Ryan89k
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