NGS data format and General Quality Control
description
Transcript of NGS data format and General Quality Control
NGS data format and General Quality Control
Data format “Flowchart”
Sequencer raw data Fastq SAM/BAM
Fastq file
• Used to record raw reads coming off the sequencers
• Each record contains four lines• Parameters were usually set by the sequencer,
such as read length
Fastq file
• Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
• Line 2 is the raw sequence letters. The read length is the length of the string.
• Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
• Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.
http://en.wikipedia.org/wiki/FASTQ_format
General quality control of raw reads
• Using FASTQC– A tool that implements some general rules– Basic Statistics– Per base sequence quality– Per sequence quality scores– Per base sequence content– Per base GC content– Per sequence GC content– Per base N content– Sequence Length Distribution– Sequence Duplication Levels– Overrepresented sequences– Kmer Content
Quality scores
Perbase “N” percentage
Sample FASTQC reports
Good quality : http://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc/fastqc_report.html
Bad quality: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/bad_sequence_fastqc/fastqc_report.html
Data format “Flowchart”
Sequencer Fastq SAM/BAM
SAM/BAM
• SAM stands for Sequence Alignment Map• BAM is the binary form of SAM• Used for mapped/aligned reads• Generated by NGS mapper/aligners
SAM
BAM