MultiQC Report

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2018-07-12, 08:31 based on data in:

/scratch/Users/magr0763/Gerber/ChIP-seq2/bbsplit/FastQC/hg38
/scratch/Users/magr0763/Gerber/ChIP-seq2/mapped
/scratch/Users/magr0763/Gerber/ChIP-seq2/qc

General Statistics

Showing ³²²/₃₂₂ rows and ⁵/₇ columns.

Sample Name	M Reads Mapped	% Aligned	% Dups	% GC	Length	% Failed	M Seqs
Ctrl_INPUT1.cat.trim	64.1
Ctrl_INPUT1_A.trim		93.3%
Ctrl_INPUT1_A_out_hg38_1			8.1%	42%	144 bp	9%	15.7
Ctrl_INPUT1_A_out_hg38_2			8.8%	42%	144 bp	9%	15.7
Ctrl_INPUT1_B.trim		93.9%
Ctrl_INPUT1_B_out_hg38_1			8.6%	42%	144 bp	9%	17.3
Ctrl_INPUT1_B_out_hg38_2			9.3%	42%	144 bp	9%	17.3
Ctrl_INPUT2.cat.trim	246.1
Ctrl_INPUT2_A.trim		92.9%
Ctrl_INPUT2_A_out_hg38_1			13.1%	41%	140 bp	9%	60.4
Ctrl_INPUT2_A_out_hg38_2			14.0%	41%	140 bp	9%	60.4
Ctrl_INPUT2_B.trim		93.4%
Ctrl_INPUT2_B_out_hg38_1			13.8%	41%	141 bp	9%	65.3
Ctrl_INPUT2_B_out_hg38_2			15.0%	41%	141 bp	9%	65.3
Ctrl_INPUT2_out_hg38_1			13.1%	41%	140 bp	9%	60.4
Ctrl_INPUT2_out_hg38_2			14.0%	41%	140 bp	9%	60.4
GR-365_Ctrl_D1.cat.trim	114.4
GR-365_Ctrl_D1_A.trim		91.9%
GR-365_Ctrl_D1_A_out_hg38_1			26.8%	41%	146 bp	9%	28.4
GR-365_Ctrl_D1_A_out_hg38_2			25.8%	41%	146 bp	9%	28.4
GR-365_Ctrl_D1_B.trim		92.6%
GR-365_Ctrl_D1_B_out_hg38_1			28.1%	41%	146 bp	9%	30.9
GR-365_Ctrl_D1_B_out_hg38_2			27.7%	41%	146 bp	9%	30.9
GR-365_Ctrl_D1_out_hg38_1			26.8%	41%	146 bp	9%	28.4
GR-365_Ctrl_D1_out_hg38_2			25.8%	41%	146 bp	9%	28.4
GR-365_Ctrl_D2.cat.trim	83.9
GR-365_Ctrl_D2_A.trim		92.8%
GR-365_Ctrl_D2_A_out_hg38_1			22.2%	42%	144 bp	9%	20.7
GR-365_Ctrl_D2_A_out_hg38_2			23.3%	42%	144 bp	9%	20.7
GR-365_Ctrl_D2_B.trim		93.3%
GR-365_Ctrl_D2_B_out_hg38_1			23.5%	42%	145 bp	9%	22.6
GR-365_Ctrl_D2_B_out_hg38_2			24.7%	43%	145 bp	9%	22.6
GR-365_Ctrl_D2_out_hg38_1			22.2%	42%	144 bp	9%	20.7
GR-365_Ctrl_D2_out_hg38_2			23.3%	42%	144 bp	9%	20.7
GR-365_Ctrl_T1.cat.trim	84.1
GR-365_Ctrl_T1_A.trim		92.3%
GR-365_Ctrl_T1_A_out_hg38_1			24.6%	40%	146 bp	9%	20.8
GR-365_Ctrl_T1_A_out_hg38_2			24.9%	40%	146 bp	9%	20.8
GR-365_Ctrl_T1_B.trim		92.8%
GR-365_Ctrl_T1_B_out_hg38_1			25.7%	40%	146 bp	9%	22.7
GR-365_Ctrl_T1_B_out_hg38_2			26.3%	40%	146 bp	9%	22.7
GR-365_Ctrl_T1_out_hg38_1			24.6%	40%	146 bp	9%	20.8
GR-365_Ctrl_T1_out_hg38_2			24.9%	40%	146 bp	9%	20.8
GR-365_Ctrl_T2.cat.trim	62.0
GR-365_Ctrl_T2_A.trim		92.5%
GR-365_Ctrl_T2_A_out_hg38_1			12.6%	41%	145 bp	9%	15.2
GR-365_Ctrl_T2_A_out_hg38_2			13.3%	41%	145 bp	9%	15.2
GR-365_Ctrl_T2_B.trim		93.1%
GR-365_Ctrl_T2_B_out_hg38_1			13.6%	41%	146 bp	9%	16.8
GR-365_Ctrl_T2_B_out_hg38_2			14.4%	41%	146 bp	9%	16.8
GR-365_Ctrl_T2_out_hg38_1			12.6%	41%	145 bp	9%	15.2
GR-365_Ctrl_T2_out_hg38_2			13.3%	41%	145 bp	9%	15.2
GR-365_Ctrl_TD1.cat.trim	58.2
GR-365_Ctrl_TD1_A.trim		92.3%
GR-365_Ctrl_TD1_A_out_hg38_1			18.0%	41%	147 bp	9%	14.3
GR-365_Ctrl_TD1_A_out_hg38_2			18.7%	42%	147 bp	9%	14.3
GR-365_Ctrl_TD1_B.trim		92.9%
GR-365_Ctrl_TD1_B_out_hg38_1			19.0%	42%	147 bp	9%	15.9
GR-365_Ctrl_TD1_B_out_hg38_2			19.8%	42%	147 bp	9%	15.9
GR-365_Ctrl_TD1_out_hg38_1			18.1%	41%	147 bp	9%	14.3
GR-365_Ctrl_TD1_out_hg38_2			18.7%	42%	147 bp	9%	14.3
GR-365_Ctrl_TD2.cat.trim	68.7
GR-365_Ctrl_TD2_A.trim		92.3%
GR-365_Ctrl_TD2_A_out_hg38_1			24.6%	41%	147 bp	9%	16.9
GR-365_Ctrl_TD2_A_out_hg38_2			25.2%	42%	147 bp	9%	16.9
GR-365_Ctrl_TD2_B.trim		92.9%
GR-365_Ctrl_TD2_B_out_hg38_1			26.4%	41%	148 bp	9%	18.8
GR-365_Ctrl_TD2_B_out_hg38_2			27.0%	42%	148 bp	9%	18.8
GR-365_Ctrl_TD2_out_hg38_1			24.6%	41%	147 bp	9%	16.9
GR-365_Ctrl_TD2_out_hg38_2			25.2%	42%	147 bp	9%	16.9
GR-365_Ctrl_V1.cat.trim	93.4
GR-365_Ctrl_V1_A.trim		92.8%
GR-365_Ctrl_V1_A_out_hg38_1			9.1%	40%	143 bp	9%	22.6
GR-365_Ctrl_V1_A_out_hg38_2			9.8%	41%	143 bp	9%	22.6
GR-365_Ctrl_V1_B.trim		93.3%
GR-365_Ctrl_V1_B_out_hg38_1			9.5%	40%	143 bp	9%	25.0
GR-365_Ctrl_V1_B_out_hg38_2			10.3%	41%	143 bp	9%	25.0
GR-365_Ctrl_V1_out_hg38_1			9.1%	40%	143 bp	9%	22.6
GR-365_Ctrl_V1_out_hg38_2			9.8%	41%	143 bp	9%	22.6
GR-365_Ctrl_V2.cat.trim	46.4
GR-365_Ctrl_V2_A.trim		92.5%
GR-365_Ctrl_V2_A_out_hg38_1			21.0%	42%	148 bp	9%	11.4
GR-365_Ctrl_V2_A_out_hg38_2			21.7%	42%	148 bp	9%	11.4
GR-365_Ctrl_V2_B.trim		93.1%
GR-365_Ctrl_V2_B_out_hg38_1			22.2%	42%	148 bp	9%	12.7
GR-365_Ctrl_V2_B_out_hg38_2			23.0%	42%	148 bp	9%	12.7
GR-365_Ctrl_V2_out_hg38_1			21.0%	42%	148 bp	9%	11.4
GR-365_Ctrl_V2_out_hg38_2			21.7%	42%	148 bp	9%	11.4
GR-365_shGR_D1.cat.trim	99.1
GR-365_shGR_D1_A.trim		92.3%
GR-365_shGR_D1_A_out_hg38_1			23.2%	41%	145 bp	9%	24.6
GR-365_shGR_D1_A_out_hg38_2			24.0%	42%	145 bp	9%	24.6
GR-365_shGR_D1_B.trim		92.9%
GR-365_shGR_D1_B_out_hg38_1			24.3%	42%	145 bp	9%	26.8
GR-365_shGR_D1_B_out_hg38_2			25.3%	42%	145 bp	9%	26.8
GR-365_shGR_D1_out_hg38_1			23.2%	41%	145 bp	9%	24.6
GR-365_shGR_D1_out_hg38_2			24.0%	42%	145 bp	9%	24.6
GR-365_shGR_D2.cat.trim	55.2
GR-365_shGR_D2_A.trim		91.4%
GR-365_shGR_D2_A_out_hg38_1			24.1%	42%	145 bp	9%	13.7
GR-365_shGR_D2_A_out_hg38_2			22.5%	42%	145 bp	9%	13.7
GR-365_shGR_D2_B.trim		92.2%
GR-365_shGR_D2_B_out_hg38_1			25.7%	42%	145 bp	9%	15.3
GR-365_shGR_D2_B_out_hg38_2			24.2%	42%	145 bp	9%	15.3
GR-365_shGR_D2_out_hg38_1			24.1%	42%	145 bp	9%	13.7
GR-365_shGR_D2_out_hg38_2			22.4%	42%	145 bp	9%	13.7
GR-365_shGR_T1.cat.trim	63.9
GR-365_shGR_T1_A.trim		92.8%
GR-365_shGR_T1_A_out_hg38_1			16.8%	42%	146 bp	9%	15.7
GR-365_shGR_T1_A_out_hg38_2			17.5%	42%	146 bp	9%	15.7
GR-365_shGR_T1_B.trim		93.4%
GR-365_shGR_T1_B_out_hg38_1			18.0%	42%	146 bp	9%	17.3
GR-365_shGR_T1_B_out_hg38_2			18.9%	42%	146 bp	9%	17.3
GR-365_shGR_T1_out_hg38_1			16.8%	42%	146 bp	9%	15.7
GR-365_shGR_T1_out_hg38_2			17.6%	42%	146 bp	9%	15.7
GR-365_shGR_T2.cat.trim	96.6
GR-365_shGR_T2_A.trim		92.5%
GR-365_shGR_T2_A_out_hg38_1			21.8%	41%	145 bp	9%	23.7
GR-365_shGR_T2_A_out_hg38_2			22.9%	41%	145 bp	9%	23.7
GR-365_shGR_T2_B.trim		93.1%
GR-365_shGR_T2_B_out_hg38_1			23.4%	41%	145 bp	9%	26.2
GR-365_shGR_T2_B_out_hg38_2			24.6%	41%	145 bp	9%	26.2
GR-365_shGR_T2_out_hg38_1			21.8%	41%	145 bp	9%	23.7
GR-365_shGR_T2_out_hg38_2			22.9%	41%	145 bp	9%	23.7
GR-365_shGR_TD1.cat.trim	88.3
GR-365_shGR_TD1_A.trim		92.1%
GR-365_shGR_TD1_A_out_hg38_1			26.0%	41%	145 bp	9%	21.8
GR-365_shGR_TD1_A_out_hg38_2			26.6%	42%	145 bp	9%	21.8
GR-365_shGR_TD1_B.trim		92.8%
GR-365_shGR_TD1_B_out_hg38_1			27.7%	41%	145 bp	9%	23.9
GR-365_shGR_TD1_B_out_hg38_2			28.5%	42%	145 bp	9%	23.9
GR-365_shGR_TD1_out_hg38_1			26.0%	41%	145 bp	9%	21.8
GR-365_shGR_TD1_out_hg38_2			26.6%	42%	145 bp	9%	21.8
GR-365_shGR_TD2.cat.trim	91.0
GR-365_shGR_TD2_A.trim		91.6%
GR-365_shGR_TD2_A_out_hg38_1			21.5%	41%	145 bp	9%	22.5
GR-365_shGR_TD2_A_out_hg38_2			20.6%	41%	145 bp	9%	22.5
GR-365_shGR_TD2_B.trim		92.3%
GR-365_shGR_TD2_B_out_hg38_1			22.9%	41%	145 bp	9%	24.8
GR-365_shGR_TD2_B_out_hg38_2			22.5%	41%	145 bp	9%	24.8
GR-365_shGR_TD2_out_hg38_1			21.5%	41%	145 bp	9%	22.5
GR-365_shGR_TD2_out_hg38_2			20.6%	41%	145 bp	9%	22.5
GR-365_shGR_V1.cat.trim	60.0
GR-365_shGR_V1_A.trim		92.5%
GR-365_shGR_V1_A_out_hg38_1			21.8%	41%	146 bp	9%	14.7
GR-365_shGR_V1_A_out_hg38_2			22.5%	41%	146 bp	9%	14.7
GR-365_shGR_V1_B.trim		93.1%
GR-365_shGR_V1_B_out_hg38_1			23.3%	41%	146 bp	9%	16.3
GR-365_shGR_V1_B_out_hg38_2			24.1%	42%	146 bp	9%	16.3
GR-365_shGR_V1_out_hg38_1			21.8%	41%	146 bp	9%	14.7
GR-365_shGR_V1_out_hg38_2			22.5%	41%	146 bp	9%	14.7
GR-365_shGR_V2.cat.trim	69.0
GR-365_shGR_V2_A.trim		92.3%
GR-365_shGR_V2_A_out_hg38_1			19.0%	41%	145 bp	9%	16.9
GR-365_shGR_V2_A_out_hg38_2			20.0%	42%	145 bp	9%	16.9
GR-365_shGR_V2_B.trim		92.9%
GR-365_shGR_V2_B_out_hg38_1			20.3%	41%	145 bp	9%	18.9
GR-365_shGR_V2_B_out_hg38_2			21.5%	42%	145 bp	9%	18.9
GR-365_shGR_V2_out_hg38_1			19.0%	41%	145 bp	9%	16.9
GR-365_shGR_V2_out_hg38_2			20.0%	42%	145 bp	9%	16.9
GR-IA1_Ctrl_D1.cat.trim	46.0
GR-IA1_Ctrl_D1_A.trim		92.3%
GR-IA1_Ctrl_D1_A_out_hg38_1			28.8%	44%	147 bp	18%	11.3
GR-IA1_Ctrl_D1_A_out_hg38_2			29.5%	44%	147 bp	18%	11.3
GR-IA1_Ctrl_D1_B.trim		92.8%
GR-IA1_Ctrl_D1_B_out_hg38_1			30.1%	44%	148 bp	18%	12.7
GR-IA1_Ctrl_D1_B_out_hg38_2			30.9%	44%	148 bp	18%	12.7
GR-IA1_Ctrl_D1_out_hg38_1			28.8%	44%	147 bp	18%	11.3
GR-IA1_Ctrl_D1_out_hg38_2			29.5%	44%	147 bp	18%	11.3
GR-IA1_Ctrl_D2.cat.trim	33.0
GR-IA1_Ctrl_D2_A.trim		92.0%
GR-IA1_Ctrl_D2_A_out_hg38_1			15.5%	44%	147 bp	18%	8.1
GR-IA1_Ctrl_D2_A_out_hg38_2			16.5%	44%	147 bp	18%	8.1
GR-IA1_Ctrl_D2_B.trim		92.6%
GR-IA1_Ctrl_D2_B_out_hg38_1			16.7%	44%	147 bp	9%	9.2
GR-IA1_Ctrl_D2_B_out_hg38_2			17.7%	44%	147 bp	18%	9.2
GR-IA1_Ctrl_D2_out_hg38_1			15.5%	44%	147 bp	18%	8.1
GR-IA1_Ctrl_D2_out_hg38_2			16.5%	44%	147 bp	18%	8.1
GR-IA1_Ctrl_T1.cat.trim	181.8
GR-IA1_Ctrl_T1_A.trim		92.7%
GR-IA1_Ctrl_T1_A_out_hg38_1			13.7%	44%	145 bp	18%	44.7
GR-IA1_Ctrl_T1_A_out_hg38_2			14.1%	44%	145 bp	18%	44.7
GR-IA1_Ctrl_T1_B.trim		93.3%
GR-IA1_Ctrl_T1_B_out_hg38_1			14.8%	44%	146 bp	18%	49.4
GR-IA1_Ctrl_T1_B_out_hg38_2			15.5%	44%	146 bp	18%	49.4
GR-IA1_Ctrl_T1_out_hg38_1			13.7%	44%	145 bp	18%	44.7
GR-IA1_Ctrl_T1_out_hg38_2			14.1%	44%	145 bp	18%	44.7
GR-IA1_Ctrl_T2.cat.trim	99.5
GR-IA1_Ctrl_T2_A.trim		92.3%
GR-IA1_Ctrl_T2_A_out_hg38_1			10.9%	43%	145 bp	9%	24.6
GR-IA1_Ctrl_T2_A_out_hg38_2			11.3%	43%	145 bp	18%	24.6
GR-IA1_Ctrl_T2_B.trim		93.0%
GR-IA1_Ctrl_T2_B_out_hg38_1			11.9%	43%	145 bp	9%	27.1
GR-IA1_Ctrl_T2_B_out_hg38_2			12.4%	44%	145 bp	18%	27.1
GR-IA1_Ctrl_T2_out_hg38_1			10.9%	43%	145 bp	9%	24.6
GR-IA1_Ctrl_T2_out_hg38_2			11.4%	43%	145 bp	18%	24.6
GR-IA1_Ctrl_TD1.cat.trim	92.5
GR-IA1_Ctrl_TD1_A.trim		92.5%
GR-IA1_Ctrl_TD1_A_out_hg38_1			26.6%	42%	148 bp	9%	22.8
GR-IA1_Ctrl_TD1_A_out_hg38_2			27.4%	43%	148 bp	9%	22.8
GR-IA1_Ctrl_TD1_B.trim		93.1%
GR-IA1_Ctrl_TD1_B_out_hg38_1			28.1%	43%	148 bp	9%	25.4
GR-IA1_Ctrl_TD1_B_out_hg38_2			29.0%	43%	148 bp	9%	25.4
GR-IA1_Ctrl_TD1_out_hg38_1			26.6%	42%	148 bp	9%	22.8
GR-IA1_Ctrl_TD1_out_hg38_2			27.4%	43%	148 bp	9%	22.8
GR-IA1_Ctrl_TD2.cat.trim	38.0
GR-IA1_Ctrl_TD2_A.trim		91.8%
GR-IA1_Ctrl_TD2_A_out_hg38_1			11.9%	43%	149 bp	9%	9.4
GR-IA1_Ctrl_TD2_A_out_hg38_2			12.0%	43%	149 bp	9%	9.4
GR-IA1_Ctrl_TD2_B.trim		92.4%
GR-IA1_Ctrl_TD2_B_out_hg38_1			12.6%	43%	149 bp	9%	10.6
GR-IA1_Ctrl_TD2_B_out_hg38_2			12.9%	43%	149 bp	18%	10.6
GR-IA1_Ctrl_TD2_out_hg38_1			11.9%	43%	149 bp	9%	9.4
GR-IA1_Ctrl_TD2_out_hg38_2			11.9%	43%	149 bp	9%	9.4
GR-IA1_Ctrl_V1.cat.trim	160.4
GR-IA1_Ctrl_V1_A.trim		92.3%
GR-IA1_Ctrl_V1_A_out_hg38_1			13.7%	44%	148 bp	18%	39.4
GR-IA1_Ctrl_V1_A_out_hg38_2			14.0%	44%	148 bp	18%	39.4
GR-IA1_Ctrl_V1_B.trim		92.9%
GR-IA1_Ctrl_V1_B_out_hg38_1			14.8%	44%	148 bp	18%	44.5
GR-IA1_Ctrl_V1_B_out_hg38_2			15.3%	44%	148 bp	18%	44.5
GR-IA1_Ctrl_V1_out_hg38_1			13.7%	44%	148 bp	18%	39.4
GR-IA1_Ctrl_V1_out_hg38_2			14.0%	44%	148 bp	18%	39.4
GR-IA1_Ctrl_V2.cat.trim	213.2
GR-IA1_Ctrl_V2_A.trim		92.6%
GR-IA1_Ctrl_V2_A_out_hg38_1			14.2%	43%	147 bp	9%	52.7
GR-IA1_Ctrl_V2_A_out_hg38_2			14.7%	44%	147 bp	18%	52.7
GR-IA1_Ctrl_V2_B.trim		93.2%
GR-IA1_Ctrl_V2_B_out_hg38_1			14.9%	43%	147 bp	18%	58.0
GR-IA1_Ctrl_V2_B_out_hg38_2			15.7%	44%	147 bp	18%	58.0
GR-IA1_Ctrl_V2_out_hg38_1			14.2%	43%	147 bp	9%	52.7
GR-IA1_Ctrl_V2_out_hg38_2			14.8%	44%	147 bp	18%	52.7
GR-IA1_shGR_D1.cat.trim	99.3
GR-IA1_shGR_D1_A.trim		92.0%
GR-IA1_shGR_D1_A_out_hg38_1			19.7%	44%	147 bp	18%	24.6
GR-IA1_shGR_D1_A_out_hg38_2			19.8%	44%	147 bp	18%	24.6
GR-IA1_shGR_D1_B.trim		92.7%
GR-IA1_shGR_D1_B_out_hg38_1			20.7%	44%	147 bp	18%	27.5
GR-IA1_shGR_D1_B_out_hg38_2			21.3%	44%	147 bp	18%	27.5
GR-IA1_shGR_D1_out_hg38_1			19.7%	44%	147 bp	18%	24.6
GR-IA1_shGR_D1_out_hg38_2			19.8%	44%	147 bp	18%	24.6
GR-IA1_shGR_D2.cat.trim	86.4
GR-IA1_shGR_D2_A.trim		92.7%
GR-IA1_shGR_D2_A_out_hg38_1			22.7%	43%	148 bp	18%	21.1
GR-IA1_shGR_D2_A_out_hg38_2			23.9%	43%	148 bp	18%	21.1
GR-IA1_shGR_D2_B.trim		93.3%
GR-IA1_shGR_D2_B_out_hg38_1			24.4%	43%	148 bp	18%	23.8
GR-IA1_shGR_D2_B_out_hg38_2			25.6%	43%	148 bp	18%	23.8
GR-IA1_shGR_D2_out_hg38_1			22.7%	43%	148 bp	18%	21.1
GR-IA1_shGR_D2_out_hg38_2			23.9%	43%	148 bp	18%	21.1
GR-IA1_shGR_T1.cat.trim	47.0
GR-IA1_shGR_T1_A.trim		92.5%
GR-IA1_shGR_T1_A_out_hg38_1			26.5%	43%	148 bp	9%	11.4
GR-IA1_shGR_T1_A_out_hg38_2			26.9%	43%	148 bp	18%	11.4
GR-IA1_shGR_T1_B.trim		93.1%
GR-IA1_shGR_T1_B_out_hg38_1			28.6%	43%	148 bp	9%	13.2
GR-IA1_shGR_T1_B_out_hg38_2			29.3%	43%	148 bp	18%	13.2
GR-IA1_shGR_T1_out_hg38_1			26.5%	43%	148 bp	9%	11.4
GR-IA1_shGR_T1_out_hg38_2			26.9%	43%	148 bp	18%	11.4
GR-IA1_shGR_T2.cat.trim	91.7
GR-IA1_shGR_T2_A.trim		92.5%
GR-IA1_shGR_T2_A_out_hg38_1			21.2%	43%	147 bp	18%	22.6
GR-IA1_shGR_T2_A_out_hg38_2			21.6%	43%	147 bp	18%	22.6
GR-IA1_shGR_T2_B.trim		93.1%
GR-IA1_shGR_T2_B_out_hg38_1			22.6%	43%	147 bp	18%	25.2
GR-IA1_shGR_T2_B_out_hg38_2			23.3%	43%	147 bp	18%	25.2
GR-IA1_shGR_T2_out_hg38_1			21.2%	43%	147 bp	18%	22.6
GR-IA1_shGR_T2_out_hg38_2			21.5%	43%	147 bp	18%	22.6
GR-IA1_shGR_TD1.cat.trim	80.4
GR-IA1_shGR_TD1_A.trim		92.2%
GR-IA1_shGR_TD1_A_out_hg38_1			21.9%	42%	147 bp	9%	19.8
GR-IA1_shGR_TD1_A_out_hg38_2			22.1%	43%	147 bp	9%	19.8
GR-IA1_shGR_TD1_B.trim		92.8%
GR-IA1_shGR_TD1_B_out_hg38_1			23.5%	43%	148 bp	9%	22.1
GR-IA1_shGR_TD1_B_out_hg38_2			23.9%	43%	148 bp	9%	22.1
GR-IA1_shGR_TD1_out_hg38_1			21.9%	42%	147 bp	9%	19.8
GR-IA1_shGR_TD1_out_hg38_2			22.1%	43%	147 bp	9%	19.8
GR-IA1_shGR_TD2.cat.trim	94.9
GR-IA1_shGR_TD2_A.trim		92.7%
GR-IA1_shGR_TD2_A_out_hg38_1			24.0%	42%	147 bp	9%	23.2
GR-IA1_shGR_TD2_A_out_hg38_2			24.9%	43%	147 bp	9%	23.2
GR-IA1_shGR_TD2_B.trim		93.3%
GR-IA1_shGR_TD2_B_out_hg38_1			25.7%	42%	147 bp	9%	26.0
GR-IA1_shGR_TD2_B_out_hg38_2			26.9%	43%	147 bp	18%	26.0
GR-IA1_shGR_TD2_out_hg38_1			24.0%	42%	147 bp	9%	23.2
GR-IA1_shGR_TD2_out_hg38_2			24.9%	43%	147 bp	9%	23.2
GR-IA1_shGR_V1.cat.trim	100.3
GR-IA1_shGR_V1_A.trim		93.2%
GR-IA1_shGR_V1_A_out_hg38_1			31.5%	43%	147 bp	18%	24.5
GR-IA1_shGR_V1_A_out_hg38_2			32.7%	43%	147 bp	18%	24.5
GR-IA1_shGR_V1_B.trim		93.8%
GR-IA1_shGR_V1_B_out_hg38_1			33.5%	43%	148 bp	18%	27.4
GR-IA1_shGR_V1_B_out_hg38_2			34.9%	43%	148 bp	18%	27.4
GR-IA1_shGR_V1_out_hg38_1			31.6%	43%	147 bp	18%	24.5
GR-IA1_shGR_V1_out_hg38_2			32.7%	43%	147 bp	18%	24.5
GR-IA1_shGR_V2.cat.trim	46.2
GR-IA1_shGR_V2_A.trim		92.2%
GR-IA1_shGR_V2_A_out_hg38_1			34.8%	44%	146 bp	18%	11.4
GR-IA1_shGR_V2_A_out_hg38_2			35.3%	44%	146 bp	18%	11.4
GR-IA1_shGR_V2_B.trim		92.7%
GR-IA1_shGR_V2_B_out_hg38_1			36.3%	44%	146 bp	18%	12.7
GR-IA1_shGR_V2_B_out_hg38_2			36.9%	44%	146 bp	18%	12.7
GR-IA1_shGR_V2_out_hg38_1			34.8%	44%	146 bp	18%	11.4
GR-IA1_shGR_V2_out_hg38_2			35.3%	44%	146 bp	18%	11.4
shGR_INPUT1.cat.trim	188.3
shGR_INPUT1_A.trim		93.2%
shGR_INPUT1_A_out_hg38_1			16.2%	41%	143 bp	9%	46.3
shGR_INPUT1_A_out_hg38_2			17.1%	41%	143 bp	9%	46.3
shGR_INPUT1_B.trim		93.8%
shGR_INPUT1_B_out_hg38_1			17.1%	41%	143 bp	9%	50.0
shGR_INPUT1_B_out_hg38_2			18.1%	41%	143 bp	9%	50.0
shGR_INPUT1_out_hg38_1			16.2%	41%	143 bp	9%	46.3
shGR_INPUT1_out_hg38_2			17.2%	41%	143 bp	9%	46.3
shGR_INPUT2.cat.trim	152.8
shGR_INPUT2_A.trim		92.8%
shGR_INPUT2_A_out_hg38_1			11.2%	41%	142 bp	9%	37.7
shGR_INPUT2_A_out_hg38_2			11.7%	41%	142 bp	9%	37.7
shGR_INPUT2_B.trim		93.5%
shGR_INPUT2_B_out_hg38_1			11.9%	41%	142 bp	9%	40.6
shGR_INPUT2_B_out_hg38_2			12.7%	41%	142 bp	9%	40.6
shGR_INPUT2_out_hg38_1			11.2%	41%	142 bp	9%	37.7
shGR_INPUT2_out_hg38_2			11.8%	41%	142 bp	9%	37.7

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools Flagstat	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	Bowtie 2	% Aligned	overall alignment rate	`overall_alignment_rate`	None
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

Preseq

Preseq estimates the complexity of a library, showing how many additional unique reads are sequenced for increasing total read count. A shallow curve indicates complexity saturation. The dashed line shows a perfectly complex library where total reads = unique reads.

Complexity curve

Note that the x axis is trimmed at the point where all the datasets show 80% of their maximum y-value, to avoid ridiculous scales.

RSeQC

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

Read Distribution

Read Distribution calculates how mapped reads are distributed over genome features.

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Samtools Flagstat

This module parses the output from samtools flagstat. All numbers in millions.

Bowtie 2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

This plot shows the number of reads aligning to the reference in different ways.
Please note that single mate alignment counts are halved to tally with pair counts properly.

There are 6 possible types of alignment: PE mapped uniquely: Pair has only one occurence in the reference genome. PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair. PE one mate mapped uniquely: One read of a pair has one occurence. PE multimapped: Pair has multiple occurence. PE one mate multimapped: One read of a pair has multiple occurence. PE neither mate aligned: Pair has no occurence.

FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

Sequence Quality Histograms

The mean quality value across each base position in the read. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Length Distribution

The distribution of fragment sizes (read lengths) found. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Sequence Duplication Levels

The relative level of duplication found for every sequence. See the FastQC help.

Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

Overrepresented sequences

The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

214 samples had less than 1% of reads made up of overrepresented sequences

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

v1.5

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Preseq

Complexity curve

RSeQC

Read Distribution

Samtools

Samtools Flagstat

Bowtie 2

FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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MultiQC Toolbox

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General Statistics

General Statistics: Columns

Preseq

Complexity curve

RSeQC

Read Distribution

Samtools

Samtools Flagstat

Bowtie 2

FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Rollover for sample name

Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

v1.5

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