ChIPseq-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 ⁸/₈ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
JLDY037D_htsStats	100.00%	93.58%	86.22%	47.85%	0.0104%	initial Stats
JLDY037E_htsStats	100.00%	95.10%	84.75%	46.01%	0.0104%	initial Stats
JLDY037F_htsStats	100.00%	95.09%	86.42%	46.66%	0.0105%	initial Stats
JLDY037G_htsStats	100.00%	94.41%	86.40%	46.88%	0.0108%	initial Stats
JLDY037I_htsStats	100.00%	95.05%	85.34%	46.28%	0.0107%	initial Stats
JLDY037J_htsStats	100.00%	93.86%	86.33%	44.32%	0.0107%	initial Stats
JLDY037K_htsStats	100.00%	95.10%	86.09%	45.04%	0.0107%	initial Stats
JLDY037L_htsStats	100.00%	61.56%	58.96%	45.31%	0.0105%	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 ⁸/₈ rows and ²/₂ columns.

Sample Name	R1 Read Lengths	R2 Read Lengths
JLDY037D_htsStats	151	151
JLDY037E_htsStats	151	151
JLDY037F_htsStats	151	151
JLDY037G_htsStats	151	151
JLDY037I_htsStats	151	151
JLDY037J_htsStats	151	151
JLDY037K_htsStats	151	151
JLDY037L_htsStats	151	151

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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_9659298609442`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_9659298609442`	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 ⁸/₈ rows and ³/₃ columns.

Sample Name	PE hits	% PE Hits	Notes
JLDY037D_htsStats	43810	0.1095%	PhiX check
JLDY037E_htsStats	21933	0.0778%	PhiX check
JLDY037F_htsStats	30137	0.0742%	PhiX check
JLDY037G_htsStats	51143	0.1469%	PhiX check
JLDY037I_htsStats	51460	0.1286%	PhiX check
JLDY037J_htsStats	36712	0.1146%	PhiX check
JLDY037K_htsStats	46331	0.1226%	PhiX check
JLDY037L_htsStats	5958	0.3030%	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 ⁸/₈ rows and ³/₃ columns.

Sample Name	% Duplicates	% Ignored	Notes
JLDY037D_htsStats	94.23%	0.04%	Remove PCR duplicates
JLDY037E_htsStats	30.68%	0.04%	Remove PCR duplicates
JLDY037F_htsStats	38.47%	0.04%	Remove PCR duplicates
JLDY037G_htsStats	52.73%	0.04%	Remove PCR duplicates
JLDY037I_htsStats	38.71%	0.04%	Remove PCR duplicates
JLDY037J_htsStats	32.84%	0.04%	Remove PCR duplicates
JLDY037K_htsStats	41.23%	0.04%	Remove PCR duplicates
JLDY037L_htsStats	91.15%	0.04%	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 ⁸/₈ rows and ⁴/₄ columns.

Sample Name	% Bp Lost	% Adapters	Avg. Bps Trimmed	Notes
JLDY037D_htsStats	0.90%	3.99%	67.93	Overlap and remove adapters
JLDY037E_htsStats	0.83%	4.15%	60.04	Overlap and remove adapters
JLDY037F_htsStats	0.85%	4.23%	60.38	Overlap and remove adapters
JLDY037G_htsStats	0.68%	3.36%	61.29	Overlap and remove adapters
JLDY037I_htsStats	1.10%	5.59%	59.37	Overlap and remove adapters
JLDY037J_htsStats	0.86%	4.23%	61.09	Overlap and remove adapters
JLDY037K_htsStats	0.78%	3.91%	60.43	Overlap and remove adapters
JLDY037L_htsStats	2.60%	9.48%	83.00	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 ⁸/₈ rows and ⁶/₆ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	% Discarded	Notes
JLDY037D_htsStats	0.02%	45.01%	54.99%	0.05	0.00%	Remove all Ns
JLDY037E_htsStats	0.01%	45.73%	54.27%	0.04	0.00%	Remove all Ns
JLDY037F_htsStats	0.01%	45.67%	54.33%	0.04	0.00%	Remove all Ns
JLDY037G_htsStats	0.01%	45.00%	55.00%	0.04	0.00%	Remove all Ns
JLDY037I_htsStats	0.01%	45.43%	54.57%	0.04	0.00%	Remove all Ns
JLDY037J_htsStats	0.01%	45.60%	54.40%	0.04	0.00%	Remove all Ns
JLDY037K_htsStats	0.01%	45.21%	54.79%	0.04	0.00%	Remove all Ns
JLDY037L_htsStats	0.02%	46.27%	53.73%	0.05	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 ⁸/₈ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	Notes
JLDY037D_htsStats	3.62%	17.99%	82.01%	10.83	Quality trim
JLDY037E_htsStats	1.17%	17.50%	82.50%	3.51	Quality trim
JLDY037F_htsStats	0.96%	21.15%	78.85%	2.89	Quality trim
JLDY037G_htsStats	1.08%	21.94%	78.06%	3.24	Quality trim
JLDY037I_htsStats	0.96%	21.35%	78.65%	2.85	Quality trim
JLDY037J_htsStats	1.04%	23.28%	76.72%	3.11	Quality trim
JLDY037K_htsStats	1.05%	20.29%	79.71%	3.13	Quality trim
JLDY037L_htsStats	27.84%	25.77%	74.23%	81.87	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 ⁸/₈ rows and ²/₂ columns.

Sample Name	% PE Lost	Notes
JLDY037D_htsStats	2.57%	Remove too short
JLDY037E_htsStats	0.64%	Remove too short
JLDY037F_htsStats	0.49%	Remove too short
JLDY037G_htsStats	0.57%	Remove too short
JLDY037I_htsStats	0.51%	Remove too short
JLDY037J_htsStats	0.56%	Remove too short
JLDY037K_htsStats	0.54%	Remove too short
JLDY037L_htsStats	34.67%	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 ⁸/₈ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
JLDY037D_htsStats	100.00%	90.60%	75.03%	47.89%	0.0000%	end Stats
JLDY037E_htsStats	100.00%	95.88%	87.69%	46.70%	0.0000%	end Stats
JLDY037F_htsStats	100.00%	95.94%	89.40%	47.44%	0.0000%	end Stats
JLDY037G_htsStats	100.00%	95.79%	89.17%	47.49%	0.0000%	end Stats
JLDY037I_htsStats	100.00%	95.91%	89.11%	47.62%	0.0000%	end Stats
JLDY037J_htsStats	100.00%	94.78%	88.77%	45.15%	0.0000%	end Stats
JLDY037K_htsStats	100.00%	95.87%	88.86%	45.76%	0.0000%	end Stats
JLDY037L_htsStats	100.00%	84.02%	61.23%	49.76%	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.

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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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ChIPseq-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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ChIPseq-cleaning-report

HTStream

Processing Overview

Preprocessing Statistics

Fragment Reduction

Basepair Reduction

hts_Stats

Table Pnbh: Columns

Read Lengths: Paired End

Table Ehgf: Columns

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener

Table Bceu: Columns

hts_SuperDeduper

Table Shtq: Columns

SuperDeduper: Duplicate Saturation

hts_AdapterTrimmer

Table Epgk: Columns

AdapterTrimmer: Trimmed Basepairs Composition

hts_NTrimmer

Table Wljs: Columns

NTrimmer: Trimmed Basepairs Composition

hts_QWindowTrim

Table Klrn: Columns

QWindowTrim: Trimmed Basepairs Composition

hts_LengthFilter

Table Auci: Columns

hts_Stats 2

Table Yaxb: Columns

Read Lengths: Paired End

Base by Cycle: Paired End

Quality by Cycle: Paired End

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