---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Management - Whole Genome Bisulfite Sequencing Data from Genewiz Received
date: '2019-04-08 12:37'
tags:
  - Panopea generosa
  - geoduck
  - Pacific oyster
  - Crassostrea gigas
  - WGBS
  - BSseq
  - bisulfite
categories:
  - 2019
  - Miscellaneous
---

Received the WGBS data from Genewiz that were [sent to Genewiz for whole genome bisulfite sequencing on 20190207](https://robertslab.github.io/sams-notebook/posts/2019/2019-02-07-Samples-Submitted---Robertos-C.gigas-DNA-for-Whole-Genome-Bisulfite-Sequencing-Genewiz/). These were from:

- Roberto's _C.gigas_ samples

| Sample_ID | Family | DNA_tube_label |
|-----------|--------|----------------|
| 0501      | 5      | 501            |
| 3501      | 35     | 3501           |
| 5201      | 52     | 5201           |
| 5901      | 59     | 5901           |
| 0502      | 5      | 5 3 A          |
| 3502      | 35     | 6 susc. 5 D3   |
| 5202      | 52     | 52 4 A         |
| 5902      | 59     | 59 11B         |
| 0503      | 5      | 05 30          |
| 3503      | 35     | 35 30          |
| 5203      | 52     | 52 30          |
| 5903      | 59     | 59 30          |

- [Yaamini's _C.gigas_](https://yaaminiv.github.io/WGBS-Samples/) samples

- [Shelly's _P.generosa_ samples](https://shellytrigg.github.io/38th-post/)

Transferred data to [nightingales/C_gigas](http://owl.fish.washington.edu/nightingales/C_gigas/) or [nightingales/P_generosa](http://owl.fish.washington.edu/nightingales/P_generosa/) and verified MD5 checksums. Have added list of files to [nightingales spreadsheet](https://docs.google.com/spreadsheets/d/1_XqIOPVHSBVGscnjzDSWUeRL7HUHXfaHxVzec-I-8Xk/edit#gid=0)(Google Sheet).

Also, of importance, are trimming guidelines for these sequences. [Hollie contacted Genewiz about their library prep](https://genefish.slack.com/archives/CD9M5LSFK/p1552084666004400) and learned they use the [Accel-NGS Methyl-Seq DNA Library Kit (Swift)](https://swiftbiosci.com/products/accel-ngs-methyl-seq-dna-library-kit/accel-ngs-methyl-seq-dna-library-kit/). Swift provides a [technical bulletin on trimming](https://swiftbiosci.com/wp-content/uploads/2016/09/16-0853-Tail-Trim-TN.pdf) and indicates the following:

> Trimming 10 bases from the beginning of both R1 and R2 _following_ adapter trimming eliminates the majority of Adaptase tails.


Here is Genewiz report:

| Table 2.1 Sample Sequencing Statistics |               |                  |          |                |                    |               |
|----------------------------------------|---------------|------------------|----------|----------------|--------------------|---------------|
|                                        |               |                  |          |                |                    |               |
| GENEWIZ NGS Data Report                |               |                  |          |                |                    |               |
|                                        |               |                  |          |                |                    |               |
| Project                                | Sample ID     | Barcode Sequence | # Reads  | Yield (Mbases) | Mean Quality Score | % Bases >= 30 |
| 30_183897003                           | 0501          | CGATGT           | 58488059 | 17547          | 35.42              | 81.73         |
| 30_183897003                           | 0502          | CAGATC           | 54841476 | 16453          | 35.43              | 81.79         |
| 30_183897003                           | 0503          | ATGTCA           | 52619991 | 15786          | 35.28              | 81.2          |
| 30_183897003                           | 3501          | TGACCA           | 51618348 | 15486          | 35.58              | 82.35         |
| 30_183897003                           | 3502          | CTTGTA           | 55001770 | 16500          | 35.54              | 82.17         |
| 30_183897003                           | 3503          | CCGTCC           | 52440884 | 15732          | 34.94              | 80.05         |
| 30_183897003                           | 5201          | ACAGTG           | 52914909 | 15874          | 35.69              | 82.72         |
| 30_183897003                           | 5202          | AGTCAA           | 47529403 | 14259          | 35.48              | 81.98         |
| 30_183897003                           | 5203          | GTCCGC           | 54386432 | 16316          | 35.08              | 80.52         |
| 30_183897003                           | 5901          | GCCAAT           | 63659740 | 19098          | 35.42              | 81.74         |
| 30_183897003                           | 5902          | AGTTCC           | 55420544 | 16626          | 35.43              | 81.8          |
| 30_183897003                           | 5903          | GTGAAA           | 54173403 | 16252          | 37.06              | 88.07         |
| 30_183897003                           | Tank2-025-026 | GCCAAT           | 66223383 | 19867          | 37.04              | 87.98         |
| 30_183897003                           | Tank3-15-16   | ACAGTG           | 49500297 | 14850          | 36.96              | 87.73         |
| 30_183897003                           | YRVA          | CGATGT           | 67542867 | 20263          | 37.1               | 88.14         |
| 30_183897003                           | YRVL          | TGACCA           | 66590575 | 19977          | 37.05              | 87.99         |