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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 1.14

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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 2025-03-07, 14:53 PST based on data in: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/E-Peve/output/02.20-E-Peve-RNAseq-alignment-HiSat2

General Statistics

Showing ⁷⁶/₇₆ rows and ²/₄ columns.

Sample Name	M Reads	M Reads Mapped	% Reads Mapped	% Aligned
POR-216-TP1-hisat2_output	46.2	41.2	89.2%
POR-216-TP1_hisat2				87.0%
POR-216-TP2-hisat2_output	45.6	42.6	93.4%
POR-216-TP2_hisat2				91.9%
POR-216-TP3-hisat2_output	40.1	37.4	93.4%
POR-216-TP3_hisat2				91.7%
POR-216-TP4-hisat2_output	54.6	52.0	95.2%
POR-216-TP4_hisat2				93.8%
POR-236-TP1-hisat2_output	51.8	48.5	93.6%
POR-236-TP1_hisat2				92.1%
POR-236-TP2-hisat2_output	50.2	48.3	96.1%
POR-236-TP2_hisat2				94.9%
POR-245-TP1-hisat2_output	46.8	43.8	93.6%
POR-245-TP1_hisat2				92.1%
POR-245-TP2-hisat2_output	42.7	41.1	96.3%
POR-245-TP2_hisat2				95.2%
POR-245-TP3-hisat2_output	48.3	45.9	95.1%
POR-245-TP3_hisat2				93.7%
POR-245-TP4-hisat2_output	40.3	35.9	89.1%
POR-245-TP4_hisat2				87.0%
POR-260-TP1-hisat2_output	40.4	36.8	91.1%
POR-260-TP1_hisat2				89.4%
POR-260-TP2-hisat2_output	43.7	41.7	95.4%
POR-260-TP2_hisat2				94.1%
POR-260-TP3-hisat2_output	42.4	40.0	94.4%
POR-260-TP3_hisat2				93.0%
POR-260-TP4-hisat2_output	47.9	45.1	94.2%
POR-260-TP4_hisat2				92.8%
POR-262-TP1-hisat2_output	49.7	45.5	91.6%
POR-262-TP1_hisat2				89.6%
POR-262-TP2-hisat2_output	50.5	47.1	93.2%
POR-262-TP2_hisat2				91.6%
POR-262-TP3-hisat2_output	53.4	50.4	94.4%
POR-262-TP3_hisat2				92.9%
POR-262-TP4-hisat2_output	43.4	41.4	95.4%
POR-262-TP4_hisat2				94.2%
POR-69-TP1-hisat2_output	55.0	51.8	94.2%
POR-69-TP1_hisat2				92.7%
POR-69-TP2-hisat2_output	49.6	47.1	94.9%
POR-69-TP2_hisat2				93.6%
POR-69-TP3-hisat2_output	53.7	51.7	96.2%
POR-69-TP3_hisat2				95.0%
POR-69-TP4-hisat2_output	43.9	42.2	96.1%
POR-69-TP4_hisat2				95.0%
POR-72-TP1-hisat2_output	39.3	34.0	86.6%
POR-72-TP1_hisat2				83.6%
POR-72-TP2-hisat2_output	40.6	31.8	78.2%
POR-72-TP2_hisat2				74.2%
POR-72-TP3-hisat2_output	50.1	46.2	92.2%
POR-72-TP3_hisat2				90.4%
POR-72-TP4-hisat2_output	55.0	51.6	93.9%
POR-72-TP4_hisat2				92.5%
POR-73-TP1-hisat2_output	50.8	48.1	94.6%
POR-73-TP1_hisat2				93.1%
POR-73-TP2-hisat2_output	55.2	52.5	95.0%
POR-73-TP2_hisat2				93.6%
POR-73-TP3-hisat2_output	50.4	48.6	96.5%
POR-73-TP3_hisat2				95.4%
POR-73-TP4-hisat2_output	46.4	44.1	95.0%
POR-73-TP4_hisat2				93.7%
POR-74-TP1-hisat2_output	44.5	41.0	92.2%
POR-74-TP1_hisat2				90.3%
POR-74-TP2-hisat2_output	44.9	43.5	96.8%
POR-74-TP2_hisat2				95.9%
POR-74-TP3-hisat2_output	55.0	52.0	94.5%
POR-74-TP3_hisat2				93.0%
POR-74-TP4-hisat2_output	50.3	48.9	97.3%
POR-74-TP4_hisat2				96.5%
POR-83-TP1-hisat2_output	44.4	41.9	94.4%
POR-83-TP1_hisat2				93.0%
POR-83-TP2-hisat2_output	47.9	44.9	93.7%
POR-83-TP2_hisat2				92.0%
POR-83-TP3-hisat2_output	47.9	45.9	95.8%
POR-83-TP3_hisat2				94.7%
POR-83-TP4-hisat2_output	59.9	57.0	95.2%
POR-83-TP4_hisat2				93.8%

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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
\|\|	Samtools	% Reads Mapped	% Reads Mapped in the bam file	`mapped_passed_pct`	None
\|\|	Bowtie 2 / HiSAT2	% Aligned	overall alignment rate	`overall_alignment_rate`	None

Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

Samtools Flagstat

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

Bowtie 2 / HiSAT2

Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4.

Paired-end alignments

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.

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General Statistics

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Paired-end alignments Help

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Paired-end alignments