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(Created page with "Mapping to a reference genome = Contents = * Overview * Mapping process: Algorithms and tools * Mapping output: SAM/BAM specification Mapping to a reference genome U Trived...")
 
 
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* Mapping process: Algorithms and tools
 
* Mapping process: Algorithms and tools
 
* Mapping output: SAM/BAM specification
 
* Mapping output: SAM/BAM specification
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Mapping to a reference genome
 
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U Trivedi 2016-05-19
 
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= The mapping process =
 
= The mapping process =
  
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Mapping to a reference genome
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[[File:mapproc.png]]
  
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U Trivedi 2016-05-19
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= Gettng a Reference sequence =
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* A reference is a consensus sequence, built up from high quality sequencing samples. This can be genome or a transcriptome.
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3
 
−
 
 
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= GeHng a Reference sequence =
 
−
* A reference is a consensus sequence, built up from high
 
−
quality sequencing samples. This can be genome or a
 
−
transcriptome.
 
 
* This should be in fasta format.
 
* This should be in fasta format.
  
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Mapping to a reference genome
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[[File:hist.png]]
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U Trivedi 2016-05-19
 
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= Mapping is a vital step =
 
= Mapping is a vital step =
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Existing Reference Sequence
 
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No Reference Sequence
 
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Short Read Alignment
 
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Variant Calling
 
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De novo Assembly
 
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De novo Transcriptome
 
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Assembly
 
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Gene Expression
 
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Metagenomics
 
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siRNA/microRNA
 
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Analysis
 
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Population Genomics
 
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…
 
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Mapping to a reference genome
 
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[[File:vital.png]]
  
 
= NGS data - Challenges =
 
= NGS data - Challenges =
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* Massive Data:
 
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* Illumina Hiseq 2500: 160GB in 2x150bp reads
 
  
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* Natural variability: SNPs, indels, de novo
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* Big Data (massive scale data):
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mutations, CNVs
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:- Illumina Hiseq 2500: 160GB in 2x150bp reads
 +
* Natural variability: SNPs, indels, de novo mutations, CNVs
 
* Sequencing errors
 
* Sequencing errors
 
* RNA-seq: splice junctions to be considered
 
* RNA-seq: splice junctions to be considered
 
* Computing resources
 
* Computing resources
  
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Mapping to a reference genome
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= Mapping process considerations 1 =
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* Different mappers depending on:
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U Trivedi 2016-05-19
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:- Read length
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:- SNVs? Indels?
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:- DNA or RNA
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:- Single end or paired end?
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= Mapping process considerations =
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:- Should multiple hits be allowed?
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Different mappers depending on:
 
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*
 
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*
 
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*
 
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*
 
−
*
 
−
 
 
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Read length
 
−
SNVs? Indels?
 
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DNA or RNA
 
−
Single end or paired end?
 
−
Should mulFple hits be allowed?
 
−
 
 
−
Which mapper to use?
 
−
Mapping to a reference genome
 
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= Mapping process considerations =
 
  
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Mapping to a reference genome
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So, which mapper to use?
  
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= Mapping process considerations 2 =
  
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8
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[[File:mappers.png]]
  
 
= Mapping algorithms =
 
= Mapping algorithms =
 
* BLAST
 
* BLAST
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:- Allows comparing and searching amino-acid and DNA sequences in a database of sequences
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* Allows comparing and searching amino-acid and DNA
+
:- Uses a heuristic algorithm: cannot guarantee the optimal alignment
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sequences in a database of sequences
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:- Too slow for NGS
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* Uses a heurisFc algorithm: cannot guarantee the
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* Hash-based mappers
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opFmal alignment
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:- High memory footprint
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* Too slow for NGS
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:- Slow for NGS
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* Based on Hashes
 
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* High memory footprint
 
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* Slow for NGS
 
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* Burrows Wheeler Transform
 
* Burrows Wheeler Transform
−
 
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:- Very fast and low memory footprint
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* Very fast and low memory footprint
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:- Very sensitive to errors
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* Very sensiFve to errors
 
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* Hybrids
 
* Hybrids
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−
Mapping to a reference genome
 
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= Mapping output =
 
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SAM/BAM format
 
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http://samtools.github.io/hts-specs/SAMv1.pdf
 
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Suppose we have the following alignment
 
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Mapping to a reference genome
 
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= Mapping output =
 
= Mapping output =
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Corresponding SAM format will be:
+
SAM format example (http://samtools.github.io/hts-specs/SAMv1.pdf)
  
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Mapping to a reference genome
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[[File:sam2panel.png]]
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= SAM/BAM format: header section =
 
= SAM/BAM format: header section =
  
−
Mapping to a reference genome
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[[File:headersec.png]]
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= SAM/BAM format: alignment section =
 
= SAM/BAM format: alignment section =
  
−
Mapping to a reference genome
+
[[File:alignsec.png]]
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= SAM/BAM format: FLAG =
 
= SAM/BAM format: FLAG =
  
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e.g. 1059, what does this mean?
+
[[File:flag.png]]
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http://broadinsFtute.github.io/picard/explain-flags.html
 
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Mapping to a reference genome
 
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U Trivedi 2016-05-19
 
  
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e.g. <code>1059</code>, what does it mean?
 +
http://broadinstitute.github.io/picard/explain-flags.html
  
 
= SAM/BAM format: CIGAR =
 
= SAM/BAM format: CIGAR =
−
* The CIGAR string is a sequence of base lengths with an associated
+
* The CIGAR string is a sequence of base lengths with an associated operation.
−
operation.
+
* Used to indicate things like which bases align (either a match/mismatch) with the reference, are deleted from the reference, and are insertions that are not in the reference.
−
* Used to indicate things like which bases align (either a match/
 
−
mismatch) with the reference, are deleted from the reference, and
 
−
are insertions that are not in the reference.
 
−
 
 
−
Mapping to a reference genome
 
−
 
 
−
U Trivedi 2016-05-19
 
−
 
 
−
15
 
  
 
= SAM/BAM format: CIGAR example =
 
= SAM/BAM format: CIGAR example =
  
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Alignment
+
[[File:cigarex.png]]
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CIGAR
 
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−
Mapping to a reference genome
 
−
 
 
−
U Trivedi 2016-05-19
 
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= SAM/BAM format: optional tags =
 
= SAM/BAM format: optional tags =
  
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Mapping to a reference genome
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[[optags1.png]]
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= SAM/BAM format: option tags =
 
= SAM/BAM format: option tags =
  
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[Image]
+
[[File:optags2.png]]
  
 
= SAM/BAM format =
 
= SAM/BAM format =
 
BAM format and BAM index
 
BAM format and BAM index
 
* BAM format
 
* BAM format
−
:- BAM format is the binary (compressed)
+
:- BAM format is the binary (compressed) representation of a SAM file.
−
representation of a SAM file
+
:- A BAM file is smaller than its corresponding SAM file, and can be read faster, but the content is the same.
−
:- A BAM file is smaller than its corresponding SAM file,
 
−
and can be read faster, but the content is the same
 
  
 
* BAM index
 
* BAM index
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= SAM/BAM format: SAM parser =
 
= SAM/BAM format: SAM parser =
 
* Samtools (http://samtools.sourceforge.net/)
 
* Samtools (http://samtools.sourceforge.net/)
−
:- Written in C (fast)
+
:- Written in C by Heng Li
−
:- Provide various uFliFes for manipulating alignments in the SAM format
+
:- Provide various utilities for manipulating alignments in the SAM format
−
* SAM to BAM conversion
+
:- SAM to BAM conversion
−
* Sorting (by coordinates or query-name)
+
:- Sorting (by coordinates or query-name)
−
* Merging several files
+
:- Merging several files
−
* BAM index
+
:- BAM index
  
−
* Picard (Java)
+
* picard-tools (essentially a version of samtools for Java)
 
* Pysam (Python)
 
* Pysam (Python)
 +
* Rsamtools (R/Bioconductor)
  
−
= Tophat2 =
+
= Tophat =
  
 
* First published 2009, up to that point, aligners behaved like so:
 
* First published 2009, up to that point, aligners behaved like so:

Latest revision as of 23:19, 8 May 2017

Mapping to a reference genome

Contents

  • Overview
  • Mapping process: Algorithms and tools
  • Mapping output: SAM/BAM specification

The mapping process

Mapproc.png

Gettng a Reference sequence

  • A reference is a consensus sequence, built up from high quality sequencing samples. This can be genome or a transcriptome.
  • This should be in fasta format.

Hist.png

Mapping is a vital step

Vital.png

NGS data - Challenges

  • Big Data (massive scale data):
- Illumina Hiseq 2500: 160GB in 2x150bp reads
  • Natural variability: SNPs, indels, de novo mutations, CNVs
  • Sequencing errors
  • RNA-seq: splice junctions to be considered
  • Computing resources

Mapping process considerations 1

  • Different mappers depending on:
- Read length
- SNVs? Indels?
- DNA or RNA
- Single end or paired end?
- Should multiple hits be allowed?

So, which mapper to use?

Mapping process considerations 2

Mappers.png

Mapping algorithms

  • BLAST
- Allows comparing and searching amino-acid and DNA sequences in a database of sequences
- Uses a heuristic algorithm: cannot guarantee the optimal alignment
- Too slow for NGS
  • Hash-based mappers
- High memory footprint
- Slow for NGS
  • Burrows Wheeler Transform
- Very fast and low memory footprint
- Very sensitive to errors
  • Hybrids

Mapping output

SAM format example (http://samtools.github.io/hts-specs/SAMv1.pdf)

Sam2panel.png

SAM/BAM format: header section

Headersec.png

SAM/BAM format: alignment section

Alignsec.png

SAM/BAM format: FLAG

Flag.png

e.g. 1059, what does it mean? http://broadinstitute.github.io/picard/explain-flags.html

SAM/BAM format: CIGAR

  • The CIGAR string is a sequence of base lengths with an associated operation.
  • Used to indicate things like which bases align (either a match/mismatch) with the reference, are deleted from the reference, and are insertions that are not in the reference.

SAM/BAM format: CIGAR example

Cigarex.png

SAM/BAM format: optional tags

optags1.png

SAM/BAM format: option tags

Optags2.png

SAM/BAM format

BAM format and BAM index

  • BAM format
- BAM format is the binary (compressed) representation of a SAM file.
- A BAM file is smaller than its corresponding SAM file, and can be read faster, but the content is the same.
  • BAM index
- Indexing a bam allows to access the alignments from a specified region.
- Required for alignment visualization soeware like IGV.

SAM/BAM format: SAM parser

- Written in C by Heng Li
- Provide various utilities for manipulating alignments in the SAM format
- SAM to BAM conversion
- Sorting (by coordinates or query-name)
- Merging several files
- BAM index
  • picard-tools (essentially a version of samtools for Java)
  • Pysam (Python)
  • Rsamtools (R/Bioconductor)

Tophat

  • First published 2009, up to that point, aligners behaved like so:
- "whenever an RNA-Seq read spans an exon boundary, part of the read will not map contiguously to the reference, which causes the mapping procedure to fail for that read."
  • Splicing-aware, finds annotated and novel junctions
  • Reaching end-0f-life ... handing over to HISAT2
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