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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.7

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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

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Report generated on 2019-04-09, 08:17 based on data in: /common/bermanblab/data/public_data/ENCODE/SNYDER_CRISPRi/ALIGNMENT/post_alignment_metrics

General Statistics

Showing ¹⁷¹/₁₇₁ rows and ⁶/₆ columns.

Sample Name	% Assigned	M Assigned	% rRNA	% mRNA	% Aligned	M Aligned
ENCSR000CPH_1	8.3%	11.1	0.0%	83.6%	83.5%	94.9
ENCSR000CPH_2	8.5%	11.9	0.0%	82.6%	83.1%	98.9
ENCSR011GAO_1	30.9%	12.3	0.0%	63.7%	79.0%	25.4
ENCSR011GAO_2	49.6%	1.6	0.0%	82.1%	81.7%	34.0
ENCSR016WFQ_1	38.0%	19.8	0.0%	81.8%	82.0%	37.3
ENCSR016WFQ_2	33.9%	13.9	0.0%	74.4%	79.7%	26.8
ENCSR024HAR_1	31.9%	15.8	0.0%	90.3%	67.4%	28.5
ENCSR024HAR_2	32.4%	10.6	0.0%	85.4%	69.5%	19.7
ENCSR028FBD_1	28.7%	14.2	0.0%	90.1%	59.1%	25.8
ENCSR028FBD_2	27.5%	12.6	0.0%	88.7%	58.9%	22.9
ENCSR039VEQ_1	34.9%	12.9	0.0%	82.2%	79.5%	24.0
ENCSR039VEQ_3	29.8%	14.6	0.0%	85.1%	65.2%	26.9
ENCSR039VEQ_4	28.4%	13.8	0.0%	85.1%	62.4%	25.3
ENCSR043UMW_3	29.8%	14.1	0.0%	75.1%	68.7%	27.6
ENCSR043UMW_4	28.4%	16.1	0.0%	72.3%	66.3%	31.9
ENCSR046FQX_1	30.0%	14.2	0.0%	85.6%	64.8%	26.5
ENCSR046FQX_2	28.9%	14.1	0.0%	84.7%	64.2%	25.9
ENCSR052BWT_1	34.2%	12.6	0.0%	64.5%	82.9%	25.9
ENCSR052BWT_2	23.7%	17.6			76.2%	36.5
ENCSR052ZPX_3	33.9%	15.5	0.0%	88.6%	72.8%	28.1
ENCSR052ZPX_4	32.5%	14.1	0.0%	88.1%	68.8%	25.6
ENCSR069OUL_1	31.4%	15.5	0.0%	73.2%	79.7%	30.3
ENCSR069OUL_2	35.7%	19.0	0.0%	76.0%	84.2%	36.7
ENCSR073QLQ_1	20.8%	11.0	0.0%	89.1%	42.3%	20.0
ENCSR073QLQ_2	26.4%	13.9	0.0%	83.3%	59.6%	25.8
ENCSR074FBG_1	21.3%	12.7	0.0%	81.5%	51.5%	23.1
ENCSR074FBG_2	19.7%	12.7	0.0%	81.7%	51.4%	23.0
ENCSR084NTT_1	37.7%	24.1	0.0%	87.6%	82.4%	43.8
ENCSR084NTT_2			0.0%	86.3%	82.2%	35.6
ENCSR095PIC_1	31.2%	9.7	0.0%	86.6%	65.3%	17.9
ENCSR095PIC_2	33.9%	15.4	0.0%	90.8%	71.4%	27.7
ENCSR096VPS_3	24.7%	11.9	0.0%	72.1%	57.6%	23.5
ENCSR096VPS_4	27.9%	9.7	0.0%	59.4%	68.5%	20.5
ENCSR103URL_1	36.6%	12.8	0.0%	90.0%	80.3%	23.1
ENCSR103URL_2	34.5%	18.5	0.0%	88.3%	78.8%	33.4
ENCSR104JMN_1	30.9%	16.2	0.0%	85.7%	64.6%	30.2
ENCSR104JMN_2	27.3%	13.0	0.0%	79.7%	58.3%	25.0
ENCSR104QKG_3	22.3%	7.8	0.0%	80.5%	55.6%	14.2
ENCSR104QKG_4	23.3%	10.0	0.0%	81.5%	56.5%	18.5
ENCSR123IMQ_1	28.0%	9.3	0.0%	88.3%	58.9%	16.8
ENCSR123IMQ_2	33.6%	12.3	0.0%	88.6%	70.9%	22.2
ENCSR126GEQ_1	19.2%	12.7	0.0%	86.6%	40.4%	23.1
ENCSR126GEQ_2	19.3%	10.7	0.0%	82.0%	46.1%	19.5
ENCSR160YSN_1	32.1%	4.5	0.0%	64.6%	78.2%	9.3
ENCSR160YSN_2	21.8%	19.1	0.0%	82.4%	46.6%	35.8
ENCSR171KMM_1	29.2%	15.5	0.0%	71.6%	80.2%	30.0
ENCSR171KMM_2	32.8%	14.3	0.0%	83.7%	71.9%	26.5
ENCSR171KMM_3	30.3%	15.3	0.0%	79.8%	67.0%	29.2
ENCSR171KMM_4	29.0%	20.6	0.0%	81.5%	65.1%	38.7
ENCSR171RTN_1	29.4%	14.4	0.0%	86.4%	68.3%	26.2
ENCSR171RTN_2	20.1%	12.7	0.0%	82.6%	52.0%	23.1
ENCSR181WYS_1	26.6%	16.3	0.0%	75.7%	77.0%	30.5
ENCSR181WYS_2	33.8%	17.0	0.0%	81.3%	78.2%	31.7
ENCSR181WYS_3	27.8%	13.9	0.0%	78.9%	63.8%	26.5
ENCSR181WYS_4	32.1%	13.5	0.0%	86.6%	73.1%	24.5
ENCSR184VVN_1	36.2%	17.8	0.0%	82.3%	80.2%	33.0
ENCSR184VVN_2	35.1%	21.7	0.0%	82.4%	77.8%	40.5
ENCSR190RZZ_1	30.3%	9.6	0.0%	85.3%	65.3%	17.7
ENCSR190RZZ_2	29.7%	12.4	0.0%	79.6%	67.7%	23.7
ENCSR200UDS_1	26.2%	11.3	0.0%	81.5%	55.7%	21.3
ENCSR200UDS_2	29.1%	11.5	0.0%	88.2%	60.5%	21.1
ENCSR223QTD_1	32.9%	14.0	0.0%	60.4%	82.6%	29.5
ENCSR223QTD_2	22.3%	13.9	0.0%	70.0%	73.2%	26.8
ENCSR235ZEI_1	35.6%	16.7	0.0%	85.9%	77.2%	30.6
ENCSR235ZEI_3			0.0%	89.0%	65.2%	30.7
ENCSR235ZEI_4	33.7%	17.3	0.0%	85.6%	74.6%	31.8
ENCSR243VNX_1	28.6%	11.7	0.0%	60.6%	79.3%	24.6
ENCSR243VNX_2	36.6%	14.2	0.0%	89.3%	79.7%	25.6
ENCSR263IOO_1	34.7%	14.6	0.0%	76.8%	80.0%	28.2
ENCSR263IOO_2	35.2%	16.2	0.0%	84.4%	80.1%	29.9
ENCSR267BHU_1	31.0%	13.4	0.0%	83.0%	66.1%	25.2
ENCSR267BHU_2	29.5%	22.2	0.0%	87.8%	61.0%	40.8
ENCSR268DNJ_1	21.9%	13.6			43.2%	24.7
ENCSR268DNJ_2	23.7%	8.3	0.0%	86.4%	49.1%	15.1
ENCSR294ZCD_1	19.3%	9.8	0.0%	79.5%	51.1%	17.9
ENCSR294ZCD_2	23.3%	9.2	0.0%	82.6%	56.8%	16.8
ENCSR299HUJ_1	37.2%	16.5	0.0%	87.7%	81.9%	30.1
ENCSR299HUJ_3	28.1%	11.6	0.0%	85.1%	64.8%	21.0
ENCSR299HUJ_4	30.9%	20.1	0.0%	84.3%	70.6%	37.1
ENCSR357LVC_3	29.4%	14.1	0.0%	67.0%	70.3%	28.7
ENCSR357LVC_4	29.0%	13.4	0.0%	87.9%	65.3%	24.1
ENCSR359VJC_1	6.7%	5.7	0.1%	52.9%	32.7%	10.4
ENCSR359VJC_2	4.1%	5.0	0.2%	40.3%	24.3%	9.3
ENCSR369BHC_1	28.8%	10.3	0.0%	64.3%	79.9%	21.1
ENCSR369BHC_2	34.3%	18.3	0.0%	86.2%	80.4%	33.4
ENCSR376CFR_1	17.3%	16.4	0.0%	75.0%	54.1%	30.4
ENCSR376CFR_2	27.0%	14.8	0.0%	81.8%	58.8%	27.9
ENCSR381TNV_1	27.1%	8.9	0.0%	88.7%	57.8%	16.1
ENCSR381TNV_2	29.7%	6.7	0.0%	89.3%	62.6%	12.2
ENCSR385ZTW_1	32.5%	18.4	0.0%	72.7%	81.3%	35.5
ENCSR385ZTW_2	34.8%	15.4	0.0%	77.7%	80.0%	29.5
ENCSR385ZTW_3	29.5%	13.4	0.0%	62.3%	72.3%	28.1
ENCSR385ZTW_4	29.3%	12.8	0.0%	67.1%	69.6%	26.0
ENCSR389OCD_1	26.4%	13.2	0.0%	86.1%	55.0%	24.6
ENCSR389OCD_2	25.9%	11.6	0.0%	91.3%	52.4%	21.0
ENCSR399QAP_1	30.9%	20.5	0.0%	82.3%	68.4%	38.6
ENCSR399QAP_2	33.3%	17.5	0.0%	78.3%	73.3%	33.9
ENCSR409OFU_1	4.6%	7.1	0.3%	42.3%	29.4%	13.1
ENCSR409OFU_2	2.4%	5.4	0.4%	27.9%	18.9%	10.3
ENCSR469EFL_1	14.3%	10.4	0.1%	76.9%	39.7%	19.0
ENCSR469EFL_2	17.9%	10.3	0.0%	80.3%	46.0%	18.7
ENCSR545HTM_1	37.0%	24.8	0.0%	77.5%	84.1%	47.5
ENCSR545HTM_2	31.2%	17.7	0.0%	86.6%	77.9%	31.9
ENCSR550FIL_1	18.2%	11.3	0.0%	79.5%	49.1%	20.6
ENCSR550FIL_2	27.8%	8.7	0.0%	88.5%	58.5%	15.7
ENCSR552HTC_1	17.4%	14.0	0.0%	86.9%	35.7%	25.3
ENCSR552HTC_2	18.1%	16.9	0.0%	84.4%	41.0%	30.5
ENCSR557BMX_1	28.1%	10.6	0.0%	82.7%	59.3%	20.1
ENCSR557BMX_2	24.1%	11.0	0.0%	89.5%	49.2%	20.0
ENCSR591QYK_1	24.6%	10.6	0.0%	85.7%	54.1%	19.2
ENCSR591QYK_2	18.5%	10.0	0.0%	77.6%	49.5%	18.5
ENCSR608ORR_1	33.9%	21.7	0.0%	86.3%	79.3%	39.7
ENCSR608ORR_2	23.9%	13.3	0.0%	78.5%	72.9%	24.5
ENCSR619EYC_1	18.5%	7.3	0.0%	81.1%	42.1%	13.6
ENCSR619EYC_2	21.6%	9.9	0.0%	85.7%	46.0%	18.0
ENCSR620DOP_1	25.9%	13.9	0.0%	86.8%	62.0%	25.3
ENCSR620DOP_2	30.4%	15.1	0.0%	88.4%	63.3%	27.7
ENCSR650QAK_1	30.9%	9.0	0.0%	86.3%	67.9%	16.3
ENCSR650QAK_3	25.6%	20.1	0.0%	82.2%	58.4%	37.3
ENCSR650QAK_4	22.4%	17.8	0.0%	82.3%	58.9%	32.3
ENCSR688UTN_1	31.8%	12.8	0.0%	78.5%	75.2%	24.3
ENCSR688UTN_3	29.1%	13.7	0.0%	88.0%	64.1%	24.8
ENCSR688UTN_4	31.2%	14.9	0.0%	89.1%	67.8%	26.9
ENCSR701TVL_1	32.9%	16.3	0.0%	83.4%	70.0%	30.6
ENCSR701TVL_2	35.8%	25.3	0.0%	83.7%	75.9%	47.5
ENCSR713AEC_1	32.5%	14.6	0.0%	67.5%	80.1%	29.5
ENCSR713AEC_2	32.3%	15.2	0.0%	61.1%	82.1%	31.8
ENCSR715EDZ_2	33.1%	13.0	0.0%	83.4%	75.5%	23.9
ENCSR715EDZ_3	21.2%	14.5	0.0%	83.8%	46.0%	26.6
ENCSR715EDZ_4	26.0%	21.9	0.0%	79.9%	60.1%	40.9
ENCSR731FEO_3	26.6%	10.0	0.0%	84.6%	61.0%	18.2
ENCSR731FEO_4	20.0%	12.7	0.0%	78.8%	57.5%	23.1
ENCSR731XIE_1	16.9%	10.2	0.0%	85.5%	35.5%	18.6
ENCSR731XIE_2	18.0%	10.6	0.0%	78.9%	46.9%	19.4
ENCSR733ROU_1	19.1%	9.6	0.0%	88.0%	40.0%	17.6
ENCSR733ROU_2	19.0%	12.4	0.0%	87.3%	39.6%	22.7
ENCSR733TFF_1	31.0%	10.7	0.0%	85.3%	66.3%	19.8
ENCSR733TFF_2	21.0%	6.9	0.0%	81.2%	44.2%	13.1
ENCSR734VBC_1	21.4%	14.9	0.0%	86.9%	47.4%	27.3
ENCSR734VBC_2	17.9%	9.1	0.0%	86.9%	38.0%	16.7
ENCSR761AQZ_1	4.3%	8.2	0.2%	40.9%	25.2%	15.3
ENCSR761AQZ_2	3.6%	7.2	0.3%	36.6%	23.5%	13.5
ENCSR773VKE_1	28.9%	13.2	0.0%	84.8%	61.4%	24.6
ENCSR773VKE_2	24.7%	23.1	0.0%	85.8%	51.8%	43.0
ENCSR781XJD_1	32.8%	17.2	0.0%	69.1%	80.7%	34.9
ENCSR781XJD_2	29.4%	17.2	0.0%	80.9%	76.7%	31.7
ENCSR800PWS_1	15.0%	11.4	0.0%	80.0%	36.0%	20.8
ENCSR800PWS_2	25.2%	8.8	0.0%	87.5%	55.0%	15.8
ENCSR808HQN_1	31.1%	20.5	0.0%	80.6%	77.3%	38.4
ENCSR808HQN_3	22.6%	11.6	0.0%	86.7%	48.7%	21.0
ENCSR808HQN_4	26.1%	14.0	0.0%	86.7%	58.1%	25.4
ENCSR810RIC_1	35.0%	11.3	0.0%	82.0%	79.4%	21.2
ENCSR810RIC_2	19.1%	15.7	0.0%	71.9%	70.7%	29.3
ENCSR819PCU_1	34.7%	18.3	0.0%	87.6%	77.6%	33.1
ENCSR819PCU_2	24.1%	7.6	0.0%	86.8%	53.0%	13.8
ENCSR819PCU_3	25.1%	8.9	0.0%	85.4%	54.9%	16.3
ENCSR850LOZ_1	32.4%	17.4	0.0%	85.3%	78.6%	31.7
ENCSR850LOZ_2	31.9%	22.8	0.0%	80.8%	79.2%	42.7
ENCSR862UHT_1	32.1%	19.2	0.0%	87.0%	67.5%	35.5
ENCSR862UHT_2	31.5%	10.3	0.0%	83.9%	66.7%	19.3
ENCSR898UNK_1	25.8%	14.2	0.0%	82.4%	57.6%	26.7
ENCSR898UNK_2	22.3%	14.5	0.0%	84.2%	51.3%	26.7
ENCSR900AQL_1	36.6%	16.4	0.0%	84.9%	76.5%	30.6
ENCSR900AQL_2	39.8%	17.6	0.0%	87.3%	80.7%	32.6
ENCSR905SEH_1	19.2%	8.9	0.0%	85.5%	43.9%	16.1
ENCSR905SEH_2	22.6%	9.5	0.0%	84.9%	52.6%	17.2
ENCSR911BML_1	34.2%	21.4	0.0%	88.3%	79.5%	38.7
ENCSR911BML_2	16.5%	13.6	0.0%	67.1%	63.1%	25.8
ENCSR942XXL_1	31.8%	13.8	0.0%	65.6%	80.0%	28.3
ENCSR942XXL_2	27.5%	17.7	0.0%	83.0%	75.7%	32.2
FAIL_EXAMPLE	0.0%	0.0	0.0%	29.3%	0.0%	0.0

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

Sort	Group	Column	Description	ID	Scale
\|\|	featureCounts	% Assigned	% Assigned reads	`percent_assigned`	None
\|\|	featureCounts	M Assigned	Assigned reads (millions)	`Assigned`	read_count
\|\|	Picard	% rRNA	Percent of aligned bases overlapping ribosomal RNA regions	`PCT_RIBOSOMAL_BASES`	None
\|\|	Picard	% mRNA	Percent of aligned bases overlapping UTRs and coding regions of mRNA transcripts	`PCT_MRNA_BASES`	None
\|\|	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	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.

featureCounts

Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

RnaSeqMetrics Assignment

Number of bases in primary alignments that align to regions in the reference genome.

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Preseq

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RnaSeqMetrics Strand Mapping

Gene Coverage

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Alignment Scores

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