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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 2025-03-08, 07:18 PST based on data in: /home/shared/8TB_HDD_01/sam/gitrepos/urol-e5/timeseries_molecular/F-Ptua/output/02.20-F-Ptua-RNAseq-alignment-HiSat2

General Statistics

Showing ⁷⁸/₇₈ rows and ²/₄ columns.

Sample Name	M Reads	M Reads Mapped	% Reads Mapped	% Aligned
POC-201-TP1-hisat2_output	41.2	29.4	71.3%
POC-201-TP1_hisat2				70.0%
POC-201-TP2-hisat2_output	45.5	30.9	67.8%
POC-201-TP2_hisat2				65.5%
POC-201-TP3-hisat2_output	32.7	14.6	44.7%
POC-201-TP3_hisat2				42.9%
POC-219-TP1-hisat2_output	42.6	28.9	68.0%
POC-219-TP1_hisat2				66.5%
POC-219-TP2-hisat2_output	38.8	24.9	64.2%
POC-219-TP2_hisat2				62.6%
POC-219-TP3-hisat2_output	42.3	7.8	18.5%
POC-219-TP3_hisat2				17.7%
POC-219-TP4-hisat2_output	39.6	22.5	56.8%
POC-219-TP4_hisat2				55.2%
POC-222-TP1-hisat2_output	40.2	29.3	73.1%
POC-222-TP1_hisat2				71.7%
POC-222-TP2-hisat2_output	45.8	30.4	66.5%
POC-222-TP2_hisat2				64.8%
POC-222-TP3-hisat2_output	47.2	34.5	73.1%
POC-222-TP3_hisat2				71.8%
POC-222-TP4-hisat2_output	34.7	23.7	68.4%
POC-222-TP4_hisat2				67.0%
POC-255-TP1-hisat2_output	39.2	26.9	68.6%
POC-255-TP1_hisat2				67.2%
POC-255-TP2-hisat2_output	41.6	27.8	66.9%
POC-255-TP2_hisat2				65.5%
POC-255-TP3-hisat2_output	49.7	25.4	51.2%
POC-255-TP3_hisat2				49.3%
POC-255-TP4-hisat2_output	42.7	30.1	70.6%
POC-255-TP4_hisat2				69.3%
POC-259-TP1-hisat2_output	37.0	22.8	61.6%
POC-259-TP1_hisat2				59.9%
POC-259-TP2-hisat2_output	43.4	27.6	63.7%
POC-259-TP2_hisat2				61.8%
POC-259-TP3-hisat2_output	45.1	29.2	64.8%
POC-259-TP3_hisat2				63.6%
POC-259-TP4-hisat2_output	39.6	28.0	70.8%
POC-259-TP4_hisat2				69.4%
POC-40-TP1-hisat2_output	37.5	26.2	69.8%
POC-40-TP1_hisat2				68.3%
POC-40-TP2-hisat2_output	43.9	30.9	70.3%
POC-40-TP2_hisat2				68.9%
POC-40-TP3-hisat2_output	42.5	29.9	70.4%
POC-40-TP3_hisat2				68.8%
POC-40-TP4-hisat2_output	39.7	28.4	71.5%
POC-40-TP4_hisat2				70.3%
POC-42-TP1-hisat2_output	37.4	25.8	69.0%
POC-42-TP1_hisat2				67.6%
POC-42-TP2-hisat2_output	45.3	31.5	69.6%
POC-42-TP2_hisat2				68.5%
POC-42-TP3-hisat2_output	40.7	29.0	71.2%
POC-42-TP3_hisat2				70.0%
POC-42-TP4-hisat2_output	33.0	18.5	56.1%
POC-42-TP4_hisat2				54.4%
POC-52-TP1-hisat2_output	32.3	5.9	18.3%
POC-52-TP1_hisat2				17.3%
POC-52-TP2-hisat2_output	43.7	29.9	68.4%
POC-52-TP2_hisat2				67.0%
POC-52-TP3-hisat2_output	37.3	25.1	67.2%
POC-52-TP3_hisat2				65.8%
POC-52-TP4-hisat2_output	36.6	26.5	72.2%
POC-52-TP4_hisat2				70.9%
POC-53-TP1-hisat2_output	40.8	27.3	66.9%
POC-53-TP1_hisat2				65.4%
POC-53-TP2-hisat2_output	39.6	26.2	66.3%
POC-53-TP2_hisat2				64.8%
POC-53-TP3-hisat2_output	43.1	30.0	69.6%
POC-53-TP3_hisat2				68.2%
POC-53-TP4-hisat2_output	40.4	23.2	57.5%
POC-53-TP4_hisat2				56.2%
POC-57-TP1-hisat2_output	38.3	26.8	70.1%
POC-57-TP1_hisat2				68.5%
POC-57-TP2-hisat2_output	39.0	23.0	58.9%
POC-57-TP2_hisat2				57.1%
POC-57-TP3-hisat2_output	45.5	32.8	72.2%
POC-57-TP3_hisat2				70.8%
POC-57-TP4-hisat2_output	42.9	32.0	74.5%
POC-57-TP4_hisat2				73.3%

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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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Bowtie 2 / HiSAT2

Paired-end alignments Help

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Paired-end alignments