---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Data Received - C.virginica Mantle MBD-BSseq from ZymoResearch
date: '2019-06-26 07:08'
tags:
  - Crassostrea virginica
  - eastern oyster
  - MBD
  - BSseq
  - mantle
categories:
  - 2019
  - Miscellaneous
---
We received the BSseq data from ZymoResearch today. Samples were [submitted on 20190326](https://robertslab.github.io/sams-notebook/posts/2019/2019-03-26-Sample-Submission-Lotterhos-C.virginica-Mantle-MBD-DNA-to-ZymoResearch-for-BSseq/). The samples constituted 24 _Crassostrea virginica_ mantle samples which were prepared using the MethylMiner Kit (Invitrogen) on [20190319](https://robertslab.github.io/sams-notebook/2019/03/19/MBD-Enrichment-DNA-Quantification-of-C.virginica-MBD-Samples-from-20190312/).

FastQ data (each file beginning with `zr2576`) for each sample was provided in three FastQ files per sample (presumably the FastQ files were split by file size limits set by ZymoResearch). I will likely concatenate the corresponding R1 and R2 files for each sample so that we simply have a single R1 and single R2 file for each sample. That will be detailed in a subsequent notebook entry when it happens.

E.g. current FastQs:

- zr2576_14_s1_R1.fastq.gz
- zr2576_14_s2_R1.fastq.gz
- zr2576_14_s3_R1.fastq.gz

Data was downloaded from ZymoResearch FTP server using FileZilla.

MD5 checksums were verified after downloading:

```shell
md5sum --check zr2576_md5_checksums.txt
```

Files were `rsync`'d to [owl/nightingales/C_virginica](https://owl.fish.washington.edu/nightingales/C_virginica/).

File info was _partially_ added to the [nightingales Google Sheet](http://b.link/nightingales). Only _partially_ due to the difficult nature of detailing FastQ data split across three files for each sample read set. This is the reason I will likely perform the FastQ concatenation - greatly simplifies data management.

The master sample sheet (Google Sheet) for the project was updated to reflect sequencing library names for each sample:

- [Roberts_2017AdultExposureSampleInfo](https://docs.google.com/spreadsheets/d/1cDLmp6jKf37gnPTwHDR07dNt-t3_jzGE2TC2afagouM/edit?usp=sharing)
