ATACseq-cleaning-report: MultiQC Report

Processing Overview

General statistics from the HTStream pipeline.

Preprocessing Statistics

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Fragment Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

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Basepair Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

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hts_Stats

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
JLAC003A_htsStats	100.00%	81.20%	79.87%	43.21%	0.0948%	initial Stats
JLAC003B_htsStats	100.00%	81.25%	78.59%	43.49%	0.1002%	initial Stats
JLAC003C_htsStats	100.00%	82.26%	78.21%	43.69%	0.1001%	initial Stats
JLAC004D_htsStats	100.00%	89.27%	87.50%	43.81%	0.1366%	initial Stats
JLAC004E_htsStats	100.00%	89.53%	88.03%	44.05%	0.1355%	initial Stats
JLAC004F_htsStats	100.00%	88.64%	87.50%	43.99%	0.1374%	initial Stats

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction1`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q301`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q301`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content1`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content1`	None
\|\|	Notes	Notes	Notes	`St_Notes1`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Notice: Each sample has a uniform read length distribution.

Showing ⁶/₆ rows and ²/₂ columns.

Sample Name	R1 Read Lengths	R2 Read Lengths
JLAC003A_htsStats	50	50
JLAC003B_htsStats	50	50
JLAC003C_htsStats	50	50
JLAC004D_htsStats	50	50
JLAC004E_htsStats	50	50
JLAC004F_htsStats	50	50

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		R1 Read Lengths	R1 Read Lengths	Length of R1 reads (uniform for each sample).	`St_Read_Lengths_R1_3732536498822`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_3732536498822`	None

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

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Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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hts_SeqScreener

A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

Showing ⁶/₆ rows and ³/₃ columns.

Sample Name	PE hits	% PE Hits	Notes
JLAC003A_htsStats	11	0.0000%	PhiX check
JLAC003B_htsStats	15	0.0000%	PhiX check
JLAC003C_htsStats	17	0.0000%	PhiX check
JLAC004D_htsStats	16	0.0000%	PhiX check
JLAC004E_htsStats	14	0.0000%	PhiX check
JLAC004F_htsStats	20	0.0000%	PhiX check

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Sort	Group	Column	Description	ID	Scale
\|\|	PE hits	PE hits	Number of Paired End Reads with Sequence	`Ss_PE_hits1`	None
\|\|	% PE Lost	% PE Hits	Percentage of Paired End Reads Lost	`Ss_PE_%_hits1`	None
\|\|	Notes	Notes	Notes	`Ss_Notes1`	None

hts_SuperDeduper

A reference free duplicate read removal tool.

Showing ⁶/₆ rows and ³/₃ columns.

Sample Name	% Duplicates	% Ignored	Notes
JLAC003A_htsStats	23.48%	3.10%	Remove PCR duplicates
JLAC003B_htsStats	23.32%	3.41%	Remove PCR duplicates
JLAC003C_htsStats	18.81%	3.06%	Remove PCR duplicates
JLAC004D_htsStats	25.64%	1.69%	Remove PCR duplicates
JLAC004E_htsStats	19.02%	1.56%	Remove PCR duplicates
JLAC004F_htsStats	16.59%	1.79%	Remove PCR duplicates

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Sort	Group	Column	Description	ID	Scale
\|\|	% Duplicates	% Duplicates	Percentage of Duplicate Reads (SE and PE)	`Sd_%_Duplicates1`	None
\|\|	% Ignored	% Ignored	Percentage of Ignored Reads (SE and PE)	`Sd_%_Ignored1`	None
\|\|	Notes	Notes	Notes	`Sd_Notes1`	None

SuperDeduper: Duplicate Saturation

Plots the number of duplicates against the number of unique reads per sample.

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hts_AdapterTrimmer

Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

Showing ⁶/₆ rows and ⁴/₄ columns.

Sample Name	% Bp Lost	% Adapters	Avg. Bps Trimmed	Notes
JLAC003A_htsStats	3.38%	39.39%	8.57	Overlap and remove adapters
JLAC003B_htsStats	3.43%	38.66%	8.87	Overlap and remove adapters
JLAC003C_htsStats	4.90%	52.01%	9.43	Overlap and remove adapters
JLAC004D_htsStats	3.55%	40.64%	8.73	Overlap and remove adapters
JLAC004E_htsStats	4.41%	47.85%	9.21	Overlap and remove adapters
JLAC004F_htsStats	5.69%	60.63%	9.39	Overlap and remove adapters

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`At_%_BP_Lost1`	None
\|\|	% Adapters	% Adapters	Percentage of Reads (SE and PE) with an Adapter	`At_%_Adapters1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of basepairs trimmed from reads	`At_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`At_Notes1`	None

AdapterTrimmer: Trimmed Basepairs Composition

Composition of basepairs trimmed from the ends of paired end and single end reads.

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hts_NTrimmer

Trims reads to the longest subsequence that contains no N's.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	% Discarded	Notes
JLAC003A_htsStats	0.08%	11.30%	88.70%	0.08	0.00%	Remove all Ns
JLAC003B_htsStats	0.09%	10.96%	89.04%	0.08	0.00%	Remove all Ns
JLAC003C_htsStats	0.08%	11.35%	88.65%	0.08	0.00%	Remove all Ns
JLAC004D_htsStats	0.07%	5.33%	94.67%	0.07	0.00%	Remove all Ns
JLAC004E_htsStats	0.08%	5.38%	94.62%	0.07	0.00%	Remove all Ns
JLAC004F_htsStats	0.07%	5.29%	94.71%	0.07	0.00%	Remove all Ns

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Nt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Nt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Nt_%_R2_BP_Lost1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Nt_Avg_BP_Trimmed1`	None
\|\|	% Discarded	% Discarded	Percentage of Reads (SE and PE) Discarded	`Nt_%_Discarded1`	None
\|\|	Notes	Notes	Notes	`Nt_Notes1`	None

NTrimmer: Trimmed Basepairs Composition

Plots the number of N bases trimmed from ends of paired end and single end reads.

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hts_QWindowTrim

Uses a sliding window approach to remove the low quality ends of reads.

Showing ⁶/₆ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	Notes
JLAC003A_htsStats	4.81%	36.06%	63.94%	4.65	Quality trim
JLAC003B_htsStats	5.35%	33.01%	66.99%	5.17	Quality trim
JLAC003C_htsStats	4.79%	30.78%	69.22%	4.55	Quality trim
JLAC004D_htsStats	3.07%	31.95%	68.05%	2.96	Quality trim
JLAC004E_htsStats	2.65%	32.62%	67.38%	2.53	Quality trim
JLAC004F_htsStats	2.46%	34.54%	65.46%	2.32	Quality trim

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Qt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R2_BP_Lost1`	None
\|\|	Avg. Bpss Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Qt_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`Qt_Notes1`	None

QWindowTrim: Trimmed Basepairs Composition

Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

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hts_LengthFilter

Discards reads below a minimum length threshold.

Showing ⁶/₆ rows and ²/₂ columns.

Sample Name	% PE Lost	Notes
JLAC003A_htsStats	36.80%	Remove too short
JLAC003B_htsStats	37.51%	Remove too short
JLAC003C_htsStats	42.16%	Remove too short
JLAC004D_htsStats	31.60%	Remove too short
JLAC004E_htsStats	33.96%	Remove too short
JLAC004F_htsStats	39.39%	Remove too short

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		% PE Lost	% PE Lost	Percentage of Paired End Reads Lost	`Lf_PE_loss1`	None
\|\|		Notes	Notes	Notes	`Lf_Notes1`	None

hts_Stats 2

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ⁶/₆ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
JLAC003A_htsStats	100.00%	94.99%	94.29%	43.35%	0.0000%	end Stats
JLAC003B_htsStats	100.00%	95.21%	93.93%	43.65%	0.0000%	end Stats
JLAC003C_htsStats	100.00%	95.65%	93.97%	43.42%	0.0000%	end Stats
JLAC004D_htsStats	100.00%	97.20%	96.42%	44.13%	0.0000%	end Stats
JLAC004E_htsStats	100.00%	97.28%	96.61%	43.98%	0.0000%	end Stats
JLAC004F_htsStats	100.00%	97.27%	96.74%	43.47%	0.0000%	end Stats

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction2`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q302`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q302`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content2`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content2`	None
\|\|	Notes	Notes	Notes	`St_Notes2`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Notice: Each sample has a uniform read length distribution.

Showing ⁶/₆ rows and ²/₂ columns.

Sample Name	R1 Read Lengths	R2 Read Lengths
JLAC003A_htsStats	50	50
JLAC003B_htsStats	50	50
JLAC003C_htsStats	50	50
JLAC004D_htsStats	50	50
JLAC004E_htsStats	50	50
JLAC004F_htsStats	50	50

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		R1 Read Lengths	R1 Read Lengths	Length of R1 reads (uniform for each sample).	`St_Read_Lengths_R1_2441693147774`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_2441693147774`	None

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

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Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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ATACseq-cleaning-report

HTStream

Processing Overview

Preprocessing Statistics

Fragment Reduction

Basepair Reduction

hts_Stats

Read Lengths: Paired End

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener

hts_SuperDeduper

SuperDeduper: Duplicate Saturation

hts_AdapterTrimmer

AdapterTrimmer: Trimmed Basepairs Composition

hts_NTrimmer

NTrimmer: Trimmed Basepairs Composition

hts_QWindowTrim

QWindowTrim: Trimmed Basepairs Composition

hts_LengthFilter

hts_Stats 2

Read Lengths: Paired End

Base by Cycle: Paired End

Quality by Cycle: Paired End

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ATACseq-cleaning-report

HTStream

Processing Overview

Preprocessing Statistics

Fragment Reduction

Basepair Reduction

hts_Stats

Table Xyrd: Columns

Read Lengths: Paired End

Table Rajd: Columns

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener

Table Plqz: Columns

hts_SuperDeduper

Table Lifn: Columns

SuperDeduper: Duplicate Saturation

hts_AdapterTrimmer

Table Ohes: Columns

AdapterTrimmer: Trimmed Basepairs Composition

hts_NTrimmer

Table Buws: Columns

NTrimmer: Trimmed Basepairs Composition

hts_QWindowTrim

Table Symi: Columns

QWindowTrim: Trimmed Basepairs Composition

hts_LengthFilter

Table Lgjm: Columns

hts_Stats 2

Table Rnzm: Columns

Read Lengths: Paired End

Table Zuir: Columns

Base by Cycle: Paired End

Quality by Cycle: Paired End

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