Data Management - Whole Genome Bisulfite Sequencing Data from Genewiz Received

Received the WGBS data from Genewiz that were sent to Genewiz for whole genome bisulfite sequencing on 20190207. 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 samples

• Shelly’s P.generosa samples

Transferred data to nightingales/C_gigas or nightingales/P_generosa and verified MD5 checksums. Have added list of files to nightingales spreadsheet(Google Sheet).

Also, of importance, are trimming guidelines for these sequences. Hollie contacted Genewiz about their library prep and learned they use the Accel-NGS Methyl-Seq DNA Library Kit (Swift). Swift provides a technical bulletin on trimming 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