Lecture 2 : Raw NGS data
quality control Vojta Bystry
vojtech.bystry@ceitec.muni.cz
Modern methods for genome analysis
(PřF:Bi7420)
NGS data analysis
22
Raw data
.fastq
Genome/Transcriptome
Reference Mapping
.bam
Interaction
analysis
CHIP-seq
Expression
analysis
RNAseq
Variant
analysis
WES
de-multiplexing
Not known
reference
QC
QC
Experiment
design
Not ”classic”
reference
Metagenomics
Reference
assembly
Immunogenetic
VDJ-genes
CRISPR
sgRNA
Methylation
Bisulfide-seq…
De-multiplexing
3
De-multiplexing
4
Primary data – fastq file
5
Fastq format - quality
6
• Fastq - q stands for quality – coded as phred score
		
Q = −10⋅log10
P
Quality Error probability
5 31%
10 10%
20 1%
30 0.1%
• What the machine things is the quality
• Only account for sequencing errors
• Very good for early problem detection
CFFFFEFFGCEEGECFGGGGAFF87@E:++6C<++3:,8,33,,:,,,:,,:,,,
Fastq – quality control
7
• How can we summarize this?
• What QC can be done?
FastQC Report
8
Fastq – quality control
9
• Fastqc - tool
10www.ceitec.eu
CEITEC
@CEITEC_Brno
Vojta Bystry
vojtech.bystry@ceitec.muni.cz
Thank you for your attention!