Final Project Checkpoint 4

Initial QC Steps

By: Fatma Gazeyoglu

To review the steps of my paper, per the data stored in PRJNA994299, 16 pigs were challenged with Swine Influenza Virus H1N2 in which samples were collected 3 from each group 2 days post inoculation (2 dpi), 3 per group at 5dpi, and the remaining 4 pigs by the end of the in vivo experiment (9 dpi) as well as an extra lung sample, adding up to a total of 33 samples. They were all run using Illumina MiSeq.

	1 Run	2 BioSample	3 AvgSpotLen	4 Bases	5 Bytes	6 Collection_Date	7 Experiment	8 isolation_source	9 Library Name	10 replicate	11 Sample Name
1	SRR25266111	SAMN36425382	265	7.54 M	3.90 Mb	2020-08-10	SRX21012101	BALF	13_BALF_EVOLSI2020	10	13_BALF_EVOLSI2020
2	SRR25266112	SAMN36425381	270	27.69 M	14.17 Mb	2020-08-09	SRX21012100	BALF	12_BALF_EVOLSI2020	9	12_BALF_EVOLSI2020
3	SRR25266113	SAMN36425380	271	3.69 M	2.30 Mb	2020-08-08	SRX21012099	BALF	11_BALF	8	11_BALF
4	SRR25266114	SAMN36425379	268	7.06 M	3.65 Mb	2020-08-07	SRX21012098	BALF	10_BALF_EVOLSI2020	7	10_BALF_EVOLSI2020
5	SRR25266115	SAMN36425378	268	11.03 M	5.67 Mb	2020-08-06	SRX21012097	BALF	09_BALF_EVOLSI2020	6	09_BALF_EVOLSI2020
6	SRR25266116	SAMN36425377	271	6.68 M	3.52 Mb	2020-08-05	SRX21012096	BALF	06_BALF	5	06_BALF
7	SRR25266117	SAMN36425405	239	4.59 M	2.20 Mb	2020-08-10	SRX21012095	MDCK cells	H1N2_EVOLSI2020	33	H1N2_EVOLSI2020
8	SRR25266118	SAMN36425404	269	6.34 M	3.34 Mb	2020-08-02	SRX21012094	nasal swab	animal16_9_NS	32	animal16_9_NS
9	SRR25266119	SAMN36425403	263	7.80 M	4.14 Mb	2020-08-01	SRX21012093	nasal swab	animal16_5_NS_EVOLSI2020	31	animal16_5_NS_EVOLSI2020
10	SRR25266120	SAMN36425376	269	5.33 M	2.80 Mb	2020-08-04	SRX21012092	BALF	05_BALF	4	05_BALF
11	SRR25266121	SAMN36425402	261	20.83 M	10.92 Mb	2020-08-10	SRX21012091	nasal swab	animal16_4_NS_EVOLSI2020	30	animal16_4_NS_EVOLSI2020
12	SRR25266122	SAMN36425401	270	15.99 M	8.21 Mb	2020-08-10	SRX21012090	nasal swab	animal16_3_NS	29	animal16_3_NS
13	SRR25266123	SAMN36425400	267	3.58 M	2.25 Mb	2020-08-07	SRX21012089	nasal swab	animal15_5_NS_EVOLSI2020	28	animal15_5_NS_EVOLSI2020
14	SRR25266124	SAMN36425399	249	6.97 M	4.40 Mb	2020-08-06	SRX21012088	nasal swab	animal15_3_NS	27	animal15_3_NS
15	SRR25266125	SAMN36425398	257	11.39 M	5.91 Mb	2020-08-04	SRX21012087	nasal swab	animal14_4_NS	26	animal14_4_NS
16	SRR25266126	SAMN36425397	266	10.94 M	5.71 Mb	2020-08-03	SRX21012086	nasal swab	animal14_3_NS	25	animal14_3_NS
17	SRR25266127	SAMN36425396	266	12.17 M	6.34 Mb	2020-08-09	SRX21012085	nasal swab	animal13_5_NS_EVOLSI2020	24	animal13_5_NS_EVOLSI2020
18	SRR25266128	SAMN36425395	259	2.12 M	1.17 Mb	2020-08-10	SRX21012084	nasal swab	animal13_4_NS	23	animal13_4_NS
19	SRR25266129	SAMN36425394	272	4.90 M	2.62 Mb	2020-08-09	SRX21012083	nasal swab	animal13_3_NS	22	animal13_3_NS
20	SRR25266130	SAMN36425393	265	4.53 M	2.47 Mb	2020-08-09	SRX21012082	nasal swab	animal12_5_NS_EVOLSI2020	21	animal12_5_NS_EVOLSI2020
21	SRR25266131	SAMN36425375	272	9.35 M	4.90 Mb	2020-08-03	SRX21012081	BALF	04_BALF	3	04_BALF
22	SRR25266132	SAMN36425392	265	2.37 M	1.27 Mb	2020-08-10	SRX21012080	nasal swab	animal12_4_NS	20	animal12_4_NS
23	SRR25266133	SAMN36425391	274	7.69 M	4.00 Mb	2020-08-09	SRX21012079	nasal swab	animal12_3_NS	19	animal12_3_NS
24	SRR25266134	SAMN36425390	264	3.58 M	1.90 Mb	2020-08-01	SRX21012078	nasal swab	animal8_4_NS	18	animal8_4_NS
25	SRR25266135	SAMN36425389	262	2.63 M	1.42 Mb	2020-08-01	SRX21012077	nasal swab	animal7_4_NS	17	animal7_4_NS
26	SRR25266136	SAMN36425388	271	27.96 M	14.42 Mb	2020-08-01	SRX21012076	nasal swab	animal7_3_NS	16	animal7_3_NS
27	SRR25266137	SAMN36425387	263	7.06 M	3.64 Mb	2020-08-01	SRX21012075	nasal swab	animal6_4_NS	15	animal6_4_NS
28	SRR25266138	SAMN36425386	263	2.94 M	1.89 Mb	2020-08-01	SRX21012074	nasal swab	animal5_5_NS	14	animal5_5_NS
29	SRR25266139	SAMN36425385	260	4.41 M	2.30 Mb	2020-08-01	SRX21012073	nasal swab	animal5_4_NS	13	animal5_4_NS
30	SRR25266140	SAMN36425384	266	9.12 M	4.69 Mb	2020-08-01	SRX21012072	nasal swab	animal5_3_NS	12	animal5_3_NS
31	SRR25266141	SAMN36425383	262	5.09 M	3.28 Mb	2020-08-10	SRX21012071	BALF	14_BALF_EVOLSI2020	11	14_BALF_EVOLSI2020
32	SRR25266142	SAMN36425374	267	15.17 M	7.77 Mb	2020-08-02	SRX21012070	BALF	02_BALF	2	02_BALF
33	SRR25266143	SAMN36425373	269	9.59 M	4.91 Mb	2020-08-01	SRX21012069	BALF	01_BALF	1	01_BALF

The samples were fastqc’d followed by trimming via trimmomatic. The following is some of the general statistics created by MultiQC post trimming.

Sample Name	% Dups	% GC	Length	M Seqs
SRR25266111_trim.1	61.0%	44%	134 bp	0.0
SRR25266111_trim.2	59.8%	44%	133 bp	0.0
SRR25266112_trim.1	75.3%	44%	136 bp	0.1
SRR25266112_trim.2	73.1%	44%	135 bp	0.1
SRR25266113_trim.1	45.9%	44%	135 bp	0.0
SRR25266113_trim.2	43.7%	44%	134 bp	0.0
SRR25266114_trim.1	60.2%	44%	135 bp	0.0
SRR25266114_trim.2	58.3%	44%	135 bp	0.0
SRR25266115_trim.1	66.5%	44%	135 bp	0.0
SRR25266115_trim.2	65.1%	44%	135 bp	0.0
SRR25266116_trim.1	57.6%	44%	136 bp	0.0
SRR25266116_trim.2	56.3%	44%	136 bp	0.0
SRR25266117_trim.1	49.1%	43%	123 bp	0.0
SRR25266117_trim.2	49.1%	43%	123 bp	0.0
SRR25266118_trim.1	64.3%	46%	135 bp	0.0
SRR25266118_trim.2	63.5%	46%	135 bp	0.0
SRR25266119_trim.1	60.7%	44%	133 bp	0.0
SRR25266119_trim.2	58.7%	44%	132 bp	0.0
SRR25266120_trim.1	54.3%	44%	135 bp	0.0
SRR25266120_trim.2	53.5%	44%	135 bp	0.0
SRR25266121_trim.1	72.0%	44%	132 bp	0.1
SRR25266121_trim.2	69.3%	44%	131 bp	0.1
SRR25266122_trim.1	71.3%	44%	136 bp	0.1
SRR25266122_trim.2	69.8%	44%	135 bp	0.1
SRR25266123_trim.1	49.2%	44%	134 bp	0.0
SRR25266123_trim.2	43.0%	44%	132 bp	0.0
SRR25266124_trim.1	50.1%	44%	125 bp	0.0
SRR25266124_trim.2	44.2%	44%	123 bp	0.0
SRR25266125_trim.1	63.7%	44%	130 bp	0.0
SRR25266125_trim.2	62.8%	44%	130 bp	0.0
SRR25266126_trim.1	68.3%	44%	134 bp	0.0
SRR25266126_trim.2	66.8%	44%	133 bp	0.0
SRR25266127_trim.1	66.7%	44%	134 bp	0.0
SRR25266127_trim.2	65.3%	44%	134 bp	0.0
SRR25266128_trim.1	44.5%	43%	131 bp	0.0
SRR25266128_trim.2	44.0%	43%	131 bp	0.0
SRR25266129_trim.1	59.0%	45%	136 bp	0.0
SRR25266129_trim.2	56.4%	45%	135 bp	0.0
SRR25266130_trim.1	53.8%	45%	133 bp	0.0
SRR25266130_trim.2	52.8%	45%	133 bp	0.0
SRR25266131_trim.1	66.2%	44%	137 bp	0.0
SRR25266131_trim.2	64.3%	44%	136 bp	0.0
SRR25266132_trim.1	39.9%	43%	134 bp	0.0
SRR25266132_trim.2	39.4%	43%	134 bp	0.0
SRR25266133_trim.1	61.1%	44%	138 bp	0.0
SRR25266133_trim.2	59.4%	44%	137 bp	0.0
SRR25266134_trim.1	51.1%	44%	133 bp	0.0
SRR25266134_trim.2	51.2%	44%	133 bp	0.0
SRR25266135_trim.1	53.4%	46%	132 bp	0.0
SRR25266135_trim.2	52.9%	46%	132 bp	0.0
SRR25266136_trim.1	78.5%	45%	137 bp	0.1
SRR25266136_trim.2	76.0%	45%	136 bp	0.1
SRR25266137_trim.1	61.8%	45%	133 bp	0.0
SRR25266137_trim.2	61.1%	45%	133 bp	0.0
SRR25266138_trim.1	38.8%	44%	131 bp	0.0
SRR25266138_trim.2	33.4%	44%	129 bp	0.0
SRR25266139_trim.1	54.3%	44%	131 bp	0.0
SRR25266139_trim.2	53.3%	44%	131 bp	0.0
SRR25266140_trim.1	64.6%	44%	134 bp	0.0
SRR25266140_trim.2	63.2%	44%	134 bp	0.0
SRR25266141_trim.1	53.5%	43%	131 bp	0.0
SRR25266141_trim.2	39.4%	44%	125 bp	0.0
SRR25266142_trim.1	68.7%	44%	135 bp	0.1
SRR25266142_trim.2	67.5%	44%	134 bp	0.1
SRR25266143_trim.1	60.8%	44%	136 bp	0.0
SRR25266143_trim.2	59.4%	44%	135 bp	0.0

It seems that the GC content is not as great but in accordance to sequencing of Influenza, the GC content tends to be around 46% so I am not worried about it for the time being.