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# System prepended metadata

title: Review info for GL MethylSeq processing
tags: [GeneLab]

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tags: GeneLab
title: Review info for GL MethylSeq processing
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# Review info for GeneLab MethylSeq processing document

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## Explanation of what this is about

Hello friends! 

We at GeneLab are putting together our "standardized" pipeline for processing MethylSeq data. If you have experience processing this datatype, we'd appreciate your set of eyes on things and any input if you have it 🙂

**Primarily we are asking for a high-level review of:**
- the general steps/planned process
- the programs/versions used
- the options we intend to include
- any general tips you know that are critical, or spots that need to be watched for, with this type of data and this processing
- any additional outputs you think are generally helpful that we should try to include
- and of course anything else you wish to voice


Internally, GeneLab's processing pipelines are stored as "**D**ata **P**rocessing **P**rotocol **D**ocuments" (DPPDs), so that is the primary document available to you for review at the stage we are at. These DPPDs are higher-level overviews, meaning they present the programs used, the general steps/process, and any options we intend to use - with most code bits being generalized templates. For actual implementation, as with our other pipelines, we will wrap this into a workflow (handling programs/environments/running code/ etc.) that will be released to all once it is finalized after this initial DPPD has been reviewed and approved. If you are inclined to go more into the weeds with things, and are having trouble or want any help with setting up programs/environments, let Mike know at Mike.Lee@nasa.gov :+1: 

## Documents

### General overview of current planned processing

Our processing is primarily based on using Bismark for identification of methylated bases (we initially drew a bit from the [nf-core/methylseq workflow](https://nf-co.re/methylseq)) and MethylKit for performing differentional methylation analysis. 

<a href="https://i.imgur.com/sgyOuXZ.png"><img src="https://i.imgur.com/sgyOuXZ.png"></a>

### DPPD document (main document to look over)
The primary DPPD document for review can be found here: https://github.com/AstrobioMike/GL-temp-stuff/blob/main/GL-DPPD-XXXX.md 

### Example outputs
The DPPD document is broken up into discretely labeled steps. If wanting to view them, examples of all the outputs we currently plan to retain for each of those steps can be found in the designated directories in this [google drive](https://drive.google.com/drive/u/0/folders/1AD7CHeQ1GW5yGHJ5RA7qInIZSbwc1Y7F). 

## How to provide feedback

Please send any suggestions/input back to the email you received pointing you here, or directly to Mike (Mike.Lee@nasa.gov) and Amanda (Amanda.M.Saravia-Butler@nasa.gov).

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**Thank you for your time and eyes 🙂**
