MultiQC Report

General Statistics

Showing ¹⁶⁵/₁₆₅ rows and ¹⁵/₁₉ columns.

Sample Name	M Reads	M Reads Mapped	dupInt	% Proper Pairs	Error rate	M Non-Primary	M Reads Mapped	% Mapped	% Proper Pairs	% MapQ 0 Reads	M Total seqs	% Aligned	M Aligned	% BP Trimmed	% Dups	% GC	Length	% Failed	M Seqs
SRR27782291	98.5	98.5	0.00%	73.5%	0.20%	21.8	76.6	100.0%	100.0%	3.4%	76.6	91.0%	36.2
SRR27782291_1														1.6%	77.8%	42%	147 bp	18%	39.8
SRR27782291_2														1.5%	79.1%	43%	147 bp	18%	39.8
SRR27782292	96.5	96.5	0.00%	83.8%	0.21%	12.7	83.8	100.0%	100.0%	1.7%	83.8	93.5%	40.4
SRR27782292_1														0.9%	78.0%	41%	148 bp	18%	43.2
SRR27782292_2														0.9%	79.0%	42%	148 bp	18%	43.2
SRR27782293	44.2	44.2	0.00%	82.5%	0.24%	6.3	37.9	100.0%	100.0%	1.9%	37.9	92.4%	18.2
SRR27782293_1														0.8%	71.0%	42%	148 bp	18%	19.7
SRR27782293_2														0.9%	72.2%	43%	148 bp	27%	19.7
SRR27782294	49.9	49.9	0.00%	73.2%	0.20%	11.3	38.6	100.0%	100.0%	3.6%	38.6	90.2%	18.3
SRR27782294_1														1.3%	69.9%	42%	148 bp	18%	20.3
SRR27782294_2														1.3%	72.0%	42%	148 bp	18%	20.3
SRR27782295	85.1	85.1	0.00%	72.9%	0.19%	19.3	65.8	100.0%	100.0%	3.5%	65.8	91.4%	31.0
SRR27782295_1														1.1%	75.9%	42%	148 bp	18%	33.9
SRR27782295_2														1.1%	77.3%	43%	148 bp	18%	33.9
SRR27782296	93.4	93.4	0.00%	89.8%	0.30%	7.2	86.2	100.0%	100.0%	0.8%	86.2	94.8%	42.0
SRR27782296_1														0.7%	70.7%	41%	148 bp	18%	44.3
SRR27782296_2														0.8%	71.1%	41%	148 bp	27%	44.3
SRR27782297	94.2	94.2	0.00%	82.7%	0.27%	13.2	81.0	100.0%	100.0%	1.9%	81.0	93.6%	39.0
SRR27782297_1														0.8%	74.4%	40%	148 bp	18%	41.6
SRR27782297_2														0.8%	74.7%	41%	148 bp	27%	41.6
SRR27782298	75.0	75.0	0.00%	82.3%	0.29%	10.8	64.2	100.0%	100.0%	1.9%	64.2	87.9%	30.9
SRR27782298_1														1.2%	73.5%	39%	148 bp	18%	35.1
SRR27782298_2														1.0%	73.2%	41%	148 bp	27%	35.1
SRR27782299	80.4	80.4	0.00%	82.3%	0.28%	11.5	68.9	100.0%	100.0%	1.9%	68.9	90.2%	33.1
SRR27782299_1														1.0%	76.1%	39%	148 bp	18%	36.7
SRR27782299_2														0.9%	76.1%	41%	148 bp	27%	36.7
SRR27782300	84.7	84.7	0.00%	82.9%	0.26%	11.7	73.1	100.0%	100.0%	1.8%	73.1	92.6%	35.2
SRR27782300_1														1.1%	75.6%	39%	148 bp	18%	38.0
SRR27782300_2														1.0%	76.1%	41%	148 bp	27%	38.0
SRR27782301	68.9	68.9	0.00%	87.1%	0.27%	7.0	62.0	100.0%	100.0%	1.2%	62.0	93.3%	30.0
SRR27782301_1														1.1%	73.2%	40%	148 bp	18%	32.2
SRR27782301_2														1.0%	73.7%	41%	148 bp	27%	32.2
SRR27782302	82.9	82.9	0.00%	86.0%	0.29%	9.2	73.7	100.0%	100.0%	1.3%	73.7	94.1%	35.7
SRR27782302_1														0.9%	72.1%	40%	148 bp	18%	37.9
SRR27782302_2														0.9%	72.8%	41%	148 bp	27%	37.9
SRR27782303	90.4	90.4	0.00%	80.7%	0.25%	14.4	76.1	100.0%	100.0%	2.2%	76.1	93.2%	36.5
SRR27782303_1														1.0%	74.8%	40%	148 bp	18%	39.2
SRR27782303_2														0.9%	75.4%	41%	148 bp	27%	39.2
SRR27782304	82.3	82.3	0.00%	84.1%	0.28%	10.5	71.8	100.0%	100.0%	1.6%	71.8	94.3%	34.6
SRR27782304_1														0.8%	72.9%	41%	148 bp	18%	36.7
SRR27782304_2														0.8%	73.2%	41%	148 bp	27%	36.7
SRR27782305	108.6	108.6	0.00%	74.4%	0.26%	22.9	85.6	100.0%	100.0%	3.2%	85.6	91.2%	40.4
SRR27782305_1														1.0%	77.7%	40%	148 bp	18%	44.3
SRR27782305_2														0.9%	77.9%	41%	148 bp	18%	44.3
SRR27782306	79.0	79.0	0.00%	81.7%	0.28%	11.8	67.2	100.0%	100.0%	2.0%	67.2	93.4%	32.3
SRR27782306_1														1.0%	72.1%	40%	148 bp	18%	34.6
SRR27782306_2														0.9%	72.3%	41%	148 bp	18%	34.6
SRR27782307	93.4	93.4	0.00%	83.6%	0.31%	12.4	81.0	100.0%	100.0%	1.7%	81.0	94.2%	39.0
SRR27782307_1														0.8%	71.0%	41%	148 bp	18%	41.5
SRR27782307_2														0.8%	71.2%	41%	148 bp	27%	41.5
SRR27782308	128.2	128.2	0.00%	52.1%	0.29%	53.2	75.0	100.0%	100.0%	8.5%	75.0	87.2%	33.4
SRR27782308_1														0.9%	73.3%	42%	148 bp	18%	38.3
SRR27782308_2														0.9%	73.5%	42%	148 bp	27%	38.3
SRR27782309	88.2	88.2	0.00%	87.8%	0.29%	8.5	79.7	100.0%	100.0%	1.1%	79.7	94.8%	38.7
SRR27782309_1														0.8%	70.7%	41%	148 bp	18%	40.8
SRR27782309_2														0.9%	71.2%	41%	148 bp	27%	40.8
SRR27782310	79.2	79.2	0.00%	87.1%	0.28%	8.1	71.0	100.0%	100.0%	1.2%	71.0	94.8%	34.5
SRR27782310_1														0.9%	71.5%	40%	148 bp	18%	36.4
SRR27782310_2														0.9%	72.4%	41%	148 bp	27%	36.4
SRR27782311	67.3	67.3	0.00%	84.7%	0.29%	8.3	59.1	100.0%	100.0%	1.5%	59.1	93.2%	28.5
SRR27782311_1														0.9%	72.5%	40%	148 bp	18%	30.6
SRR27782311_2														0.9%	73.5%	42%	148 bp	27%	30.6
SRR27782312	58.4	58.4	0.00%	89.5%	0.29%	4.7	53.7	100.0%	100.0%	0.8%	53.7	92.7%	26.1
SRR27782312_1														1.1%	75.8%	40%	148 bp	18%	28.2
SRR27782312_2														1.0%	75.7%	41%	148 bp	27%	28.2
SRR27782313	71.8	71.8	0.00%	84.5%	0.26%	8.9	62.9	100.0%	100.0%	1.5%	62.9	93.9%	30.4
SRR27782313_1														0.9%	71.0%	41%	148 bp	18%	32.3
SRR27782313_2														0.9%	72.6%	42%	148 bp	27%	32.3
SRR27782314	112.9	112.9	0.00%	61.7%	0.30%	37.0	75.9	100.0%	100.0%	6.0%	75.9	87.2%	34.8
SRR27782314_1														0.7%	72.1%	41%	148 bp	18%	40.0
SRR27782314_2														0.8%	72.3%	42%	148 bp	27%	40.0
SRR27782315	81.8	81.8	0.00%	87.3%	0.29%	8.2	73.6	100.0%	100.0%	1.1%	73.6	94.2%	35.7
SRR27782315_1														0.8%	71.6%	40%	148 bp	18%	37.9
SRR27782315_2														0.8%	71.9%	41%	148 bp	27%	37.9
SRR27782316	115.4	115.4	0.00%	86.1%	0.27%	12.7	102.7	100.0%	100.0%	1.3%	102.7	94.0%	49.7
SRR27782316_1														0.8%	76.4%	40%	148 bp	18%	52.9
SRR27782316_2														0.8%	76.4%	41%	148 bp	27%	52.9
SRR27782317	83.5	83.5	0.00%	88.4%	0.27%	7.5	76.0	100.0%	100.0%	1.0%	76.0	94.7%	36.9
SRR27782317_1														0.8%	70.4%	41%	148 bp	18%	39.0
SRR27782317_2														0.8%	71.3%	41%	148 bp	18%	39.0
SRR27782318	90.8	90.8	0.00%	89.0%	0.25%	7.7	83.0	100.0%	100.0%	0.9%	83.0	95.0%	40.4
SRR27782318_1														0.9%	71.7%	41%	148 bp	18%	42.5
SRR27782318_2														0.8%	72.5%	42%	148 bp	27%	42.5
SRR27782319	83.2	83.2	0.00%	84.7%	0.27%	10.2	73.1	100.0%	100.0%	1.5%	73.1	93.9%	35.3
SRR27782319_1														0.8%	74.7%	40%	148 bp	18%	37.6
SRR27782319_2														0.8%	74.8%	41%	148 bp	27%	37.6
SRR27782320	85.2	85.2	0.00%	84.9%	0.28%	10.3	74.9	100.0%	100.0%	1.5%	74.9	93.8%	36.2
SRR27782320_1														0.9%	72.4%	40%	148 bp	18%	38.6
SRR27782320_2														0.8%	72.6%	41%	148 bp	27%	38.6
SRR27782321	90.2	90.2	0.00%	85.0%	0.30%	10.9	79.2	100.0%	100.0%	1.5%	79.2	93.8%	38.3
SRR27782321_1														0.8%	74.8%	40%	148 bp	18%	40.9
SRR27782321_2														0.8%	73.8%	41%	148 bp	27%	40.9
SRR27782322	85.9	85.9	0.00%	88.1%	0.30%	7.7	78.2	100.0%	100.0%	0.9%	78.2	93.7%	37.9
SRR27782322_1														0.9%	76.3%	40%	148 bp	18%	40.4
SRR27782322_2														0.9%	75.7%	41%	148 bp	27%	40.4
SRR27782323	70.5	70.5	0.00%	89.5%	0.28%	5.6	64.9	100.0%	100.0%	0.8%	64.9	94.7%	31.5
SRR27782323_1														0.8%	73.4%	41%	148 bp	18%	33.3
SRR27782323_2														0.9%	74.3%	42%	148 bp	27%	33.3
SRR27782324	91.9	91.9	0.00%	88.1%	0.31%	8.6	83.3	100.0%	100.0%	1.1%	83.3	94.6%	40.5
SRR27782324_1														0.6%	72.3%	40%	149 bp	18%	42.8
SRR27782324_2														0.7%	72.7%	41%	148 bp	27%	42.8
SRR27782325	62.5	62.5	0.00%	85.2%	0.28%	7.3	55.1	100.0%	100.0%	1.4%	55.1	94.0%	26.6
SRR27782325_1														0.8%	69.4%	41%	148 bp	18%	28.3
SRR27782325_2														0.9%	70.9%	42%	148 bp	27%	28.3
SRR27782326	59.5	59.5	0.00%	88.6%	0.26%	5.2	54.2	100.0%	100.0%	0.9%	54.2	95.0%	26.3
SRR27782326_1														0.9%	72.1%	41%	148 bp	18%	27.7
SRR27782326_2														1.0%	73.5%	42%	148 bp	27%	27.7
SRR27782327	115.9	115.9	0.00%	79.1%	0.22%	19.8	96.1	100.0%	100.0%	2.3%	96.1	93.3%	45.8
SRR27782327_1														1.2%	79.3%	42%	148 bp	18%	49.1
SRR27782327_2														1.2%	80.9%	43%	148 bp	27%	49.1
SRR27782328	119.1	119.1	0.00%	82.5%	0.23%	16.9	102.2	100.0%	100.0%	1.8%	102.2	94.2%	49.1
SRR27782328_1														0.9%	80.3%	42%	148 bp	18%	52.2
SRR27782328_2														0.9%	81.6%	42%	148 bp	27%	52.2
SRR27782329	51.0	51.0	0.00%	78.2%	0.25%	9.1	41.9	100.0%	100.0%	2.5%	41.9	92.2%	20.0
SRR27782329_1														0.9%	71.6%	42%	148 bp	18%	21.6
SRR27782329_2														0.8%	72.9%	43%	148 bp	18%	21.6
SRR27782330	74.2	74.2	0.00%	86.6%	0.28%	7.9	66.3	100.0%	100.0%	1.3%	66.3	90.9%	32.1
SRR27782330_1														0.8%	67.6%	41%	148 bp	18%	35.4
SRR27782330_2														0.8%	67.6%	42%	148 bp	18%	35.4
SRR27782331	103.4	103.4	0.00%	79.1%	0.38%	17.8	85.6	100.0%	100.0%	2.5%	85.6	91.9%	40.9
SRR27782331_1														0.7%	76.4%	40%	148 bp	18%	44.5
SRR27782331_2														0.8%	72.4%	41%	148 bp	27%	44.5
SRR27782332	88.4	88.4	0.00%	87.9%	0.31%	8.4	80.1	100.0%	100.0%	1.1%	80.1	93.6%	38.9
SRR27782332_1														0.9%	74.8%	40%	148 bp	18%	41.5
SRR27782332_2														0.9%	73.3%	41%	148 bp	27%	41.5
SRR27782333	93.9	93.9	0.00%	83.9%	0.31%	12.2	81.6	100.0%	100.0%	1.7%	81.6	93.7%	39.4
SRR27782333_1														0.8%	71.8%	39%	148 bp	18%	42.1
SRR27782333_2														0.9%	72.2%	40%	148 bp	27%	42.1
SRR27782334	89.8	89.8	0.00%	84.2%	0.30%	11.4	78.3	100.0%	100.0%	1.6%	78.3	94.1%	37.8
SRR27782334_1														0.9%	72.1%	40%	148 bp	18%	40.2
SRR27782334_2														0.9%	72.0%	41%	148 bp	27%	40.2
SRR27782335	79.4	79.4	0.00%	83.8%	0.28%	10.5	69.0	100.0%	100.0%	1.7%	69.0	93.8%	33.3
SRR27782335_1														0.7%	72.8%	41%	149 bp	18%	35.5
SRR27782335_2														0.7%	72.6%	41%	148 bp	27%	35.5
SRR27782336	134.0	134.0	0.00%	49.1%	0.28%	58.9	75.1	100.0%	100.0%	9.8%	75.1	85.1%	32.9
SRR27782336_1														0.8%	76.4%	41%	148 bp	18%	38.7
SRR27782336_2														0.8%	76.5%	42%	148 bp	27%	38.7
SRR27782337	86.7	86.7	0.00%	76.2%	0.27%	17.3	69.5	100.0%	100.0%	3.0%	69.5	92.0%	33.0
SRR27782337_1														0.9%	75.9%	40%	148 bp	18%	35.9
SRR27782337_2														0.8%	75.6%	41%	148 bp	27%	35.9
SRR27782338	90.1	90.1	0.00%	72.2%	0.26%	20.9	69.2	100.0%	100.0%	3.6%	69.2	90.6%	32.6
SRR27782338_1														1.3%	75.0%	38%	148 bp	27%	35.9
SRR27782338_2														1.1%	75.6%	40%	148 bp	18%	35.9
SRR27782339	81.8	81.8	0.00%	88.5%	0.32%	7.3	74.5	100.0%	100.0%	1.0%	74.5	94.8%	36.2
SRR27782339_1														0.8%	69.7%	40%	148 bp	18%	38.2
SRR27782339_2														0.9%	69.7%	41%	148 bp	27%	38.2
SRR27782340	91.6	91.6	0.00%	79.8%	0.32%	15.3	76.4	100.0%	100.0%	2.3%	76.4	93.2%	36.6
SRR27782340_1														0.8%	72.2%	41%	148 bp	18%	39.3
SRR27782340_2														0.8%	72.0%	41%	148 bp	27%	39.3
SRR27782341	162.0	162.0	0.00%	51.2%	0.34%	68.2	93.8	100.0%	100.0%	8.5%	93.8	85.3%	41.5
SRR27782341_1														0.9%	76.0%	41%	148 bp	18%	48.7
SRR27782341_2														1.0%	74.9%	42%	148 bp	27%	48.7
SRR27782342	89.9	89.9	0.00%	83.2%	0.29%	12.3	77.7	100.0%	100.0%	1.8%	77.7	94.2%	37.5
SRR27782342_1														0.9%	72.1%	40%	148 bp	18%	39.8
SRR27782342_2														1.0%	72.8%	41%	148 bp	27%	39.8
SRR27782343	85.4	85.4	0.00%	87.5%	0.32%	8.4	77.0	100.0%	100.0%	1.2%	77.0	94.4%	37.4
SRR27782343_1														0.8%	73.4%	40%	148 bp	18%	39.6
SRR27782343_2														0.8%	72.9%	41%	148 bp	27%	39.6
SRR27782344	107.5	107.5	0.00%	53.1%	0.31%	43.6	64.0	100.0%	100.0%	8.5%	64.0	86.1%	28.6
SRR27782344_1														0.9%	73.8%	38%	148 bp	27%	33.1
SRR27782344_2														0.9%	74.2%	40%	148 bp	27%	33.1
SRR27782345	92.3	92.3	0.00%	88.3%	0.27%	8.4	83.9	100.0%	100.0%	1.0%	83.9	94.7%	40.8
SRR27782345_1														0.7%	78.0%	40%	148 bp	18%	43.0
SRR27782345_2														0.8%	78.6%	41%	148 bp	27%	43.0

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	M Reads	Total reads in the bam file (millions)	`flagstat_total`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	DupRadar	dupInt	Intercept value from DupRadar	`dupRadar_intercept`	None
\|\|	RSeQC	% Proper Pairs	% Reads mapped in proper pairs	`proper_pairs_percent`	None
\|\|	Samtools	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	Samtools	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	Samtools	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	Samtools	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	Samtools	% Proper Pairs	% Properly Paired Reads	`reads_properly_paired_percent`	None
\|\|	Samtools	% MapQ 0 Reads	% of Reads that are Ambiguously Placed (MapQ=0)	`reads_MQ0_percent`	None
\|\|	Samtools	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count
\|\|	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count
\|\|	Cutadapt	% BP Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	FastQC (trimmed)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (trimmed)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (trimmed)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (trimmed)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (trimmed)	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

STAR_SALMON DESeq2 PCA plot

PCA plot between samples in the experiment. These values are calculated using DESeq2 in the deseq2_qc.r script.

loading..

STAR_SALMON DESeq2 sample similarity

is generated from clustering by Euclidean distances between DESeq2 rlog values for each sample in the deseq2_qc.r script.

loading..

DupRadar

provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.

loading..

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.

loading..

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.

loading..

Inner Distance

Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

loading..

Read Duplication

read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

loading..

Junction Annotation

Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

loading..

Junction Saturation

Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

Click a line to see the data side by side (as in the original RSeQC plot).

loading..

Infer experiment

Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

loading..

Bam Stat

All numbers reported in millions.

loading..

Samtools

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

Percent Mapped

Alignment metrics from samtools stats; mapped vs. unmapped reads.

For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

loading..

Alignment metrics

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

loading..

Samtools Flagstat

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

loading..

Mapped reads per contig

The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

loading..

STAR

STAR is an ultrafast universal RNA-seq aligner.

Alignment Scores

loading..

Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

Filtered Reads

This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

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

Trimmed Sequence Lengths

This plot shows the number of reads with certain lengths of adapter trimmed.

Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

See the cutadapt documentation for more information on how these numbers are generated.

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

v1.10.1

MultiQC Toolbox

Highlight Samples

Rename Samples

Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

STAR_SALMON DESeq2 PCA plot

STAR_SALMON DESeq2 sample similarity

DupRadar

Preseq

Complexity curve

RSeQC

Read Distribution

Inner Distance

Read Duplication

Junction Annotation

Junction Saturation

Infer experiment

Bam Stat

Samtools

Percent Mapped

Alignment metrics

Samtools Flagstat

Mapped reads per contig

STAR

Alignment Scores

Cutadapt

Filtered Reads

Trimmed Sequence Lengths

Toggle navigation v1.10.1

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Export Plots

Choose Plots

Save Settings

Load Settings

About MultiQC

General Statistics

General Statistics: Columns

STAR_SALMON DESeq2 PCA plot

STAR_SALMON DESeq2 sample similarity

DupRadar

Preseq

Complexity curve

RSeQC

Read Distribution

Inner Distance

Read Duplication

Junction Annotation

Junction Saturation

Infer experiment

Bam Stat

Samtools

Percent Mapped Help

Alignment metrics

Samtools Flagstat

Mapped reads per contig

STAR

Alignment Scores

Cutadapt

Filtered Reads

Trimmed Sequence Lengths Help

v1.10.1

Highlight Samples

Rename Samples

Show / Hide Samples

Percent Mapped

Trimmed Sequence Lengths