---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Analysis - C.virginica MBD Sequencing Coverage
date: '2019-04-18 13:54'
tags:
  - Crassostrea virginica
  - Eastern oyster
  - MBD
  - Bismark
  - jupyter
categories:
  - 2019
  - Miscellaneous
---
A while ago, Steven tasked me with assessing some questions related to the sequencing coverage we get doing MBD-BSseq in this [GitHub issue](https://github.com/RobertsLab/resources/issues/609). At the heart of it all was really to try to get an idea of how much usable data we actually get when we do an MBD-BSseq project. Yaamini happened to have done an MBD-BSseq project relatively recently, and it's one she's actively working on analyzing, so we went with that data set.

Data was initially trimmed:

- [20180411 TrimGalore and FastQC](https://robertslab.github.io/sams-notebook/posts/2018/2018-04-11-trimgalorefastqcmultiqc-trim-10bp-53-ends-c-virginica-mbd-bs-seq-fastq-data/)

Subsequently, the data was concatenated, subset, and aligned using Bismark:

- [20190313 Bismark alignment subsetting](https://robertslab.github.io/sams-notebook/posts/2019/2019-03-13-Methylation-Analysis---C.virginica-Gonad-MBD-with-Varying-Read-Subsets-with-Bismark-on-Mox/)


Today, I finally found the time to dedicate to evaluating alignment coverage of each of the Bismark sequence subsets. It was done in a Jupyter Notebook and solely with Bash/Python! I used this as project as an excuse to dive into using Python a bit more, instead of using R. For what I needed to accomplish, I just felt like this approach was simpler (instead of creating an R project and all of that).

- [20190418_cvir_mbd_coverage_comparison.ipynb](https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190418_cvir_mbd_coverage_comparison.ipynb) (GitHub)

---

# RESULTS

Plot of the various "Percent Methylation" coverages in each of the Bismark subsets. The lines/bars are redundant. I added the lines to provide a better visual guide to see how the percent methylation coverage changes from one Bismark subset to the next. A quick guide to X axis labeling:

- half_avg_reads: Subset of 50% of the average number of read pairs.

- avg_reads: Subset of the average number of read pairs.

- half_total_reads: Subset of 50% of the total number of read pairs.

- total_reads: All read pairs.

![Bar/line plot showing differences in percent CpG coverage of each Bismark subset](https://github.com/RobertsLab/sams-notebook/blob/master/images/screencaps/20190418_cvir_mbd_cov_comparison.png?raw=true)


---

##### Summary Table

| Bismark Subset                | No. of Read pairs | Trimmed read length (bp) | No. of Bases (Gbp) | Genome size (Gbp) | Genome coverage (x fold) | Mean CpG Coverage | Percent CpG Coverage | Percent 5x CpG Coverage | Percent 10x CpG Coverage |
|-------------------------------|-------------------|--------------------------|--------------------|-------------------|--------------------------|-------------------|----------------------|-------------------------|--------------------------|
| total_reads_CpG_coverage      | 275914272         | 80                       | 22.07              | 0.684741          | 32.24                    | 7.3               | 45.3                 | 14.7                    | 9.1                      |
| half_total_reads_CpG_coverage | 137957136         | 80                       | 11.04              | 0.684741          | 16.12                    | 3.5               | 33.5                 | 9.2                     | 5.7                      |
| avg_reads_CpG_coverage        | 27591427          | 80                       | 2.21               | 0.684741          | 3.22                     | 0.7               | 15.3                 | 3.2                     | 1.8                      |
| half_avg_reads_CpG_coverage   | 13795713          | 80                       | 1.10               | 0.684741          | 1.61                     | 0.5               | 11.2                 | 2.3                     | 1.2                      |


---

After looking at this a bit, it's surprising how little coverage we actually end up with. This is data for _all_ of the samples combined (n = 10), 100bp PE sequencing. This helps inform us on how much sequencing we actually need to do in order to achieve a target coverage.

_However_, this analysis doesn't tell us anything about methylated CpG coverage (although, it could if I tweaked things a tiny bit). Yaamini has been working on that, so she should have those answers. Her analysis and my analysis will likely be used to contribute to our [BS-seq decision tree](https://github.com/RobertsLab/resources/issues/543).
