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There are 17 contigs. |
Aligner overview
There are many aligners available, but we will concentrate on two of the most popular general-purpose ones: bwa and bowtie2. The table below outlines the available protocols for them.
alignment type | aligner options | pro's | con's |
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global with bwa | SE: PE: - bwa aln <R1>
- bwa aln <R2>
- bwa sampe
| - simple to use (take default options)
- good for basic global alignment
| |
global with bowtie2 | bowtie2 --global | - extremely configurable
- can be used for RNAseq alignment because of its many options
| |
local with bwa | bwa mem | - simple to use (take default options)
- very fast
- no adapter trimming needed
- good for simple RNAseq analysis
- the secondary alignments it reports provide splice junction information
| - always produces alignments with secondary reads
- must be filtered if not desired
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local with bowtie2 | bowtie2 --local | - extremely configurable
- no adapter trimming needed
- good for small RNA alignment because of its many options
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Exercise #1: BWA global alignment – Yeast ChIP-seq
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