Other mappers

The BWA aligner is available at http://bio-bwa.sourceforge.net/, or (for the course) you can download it from here with curl:

Installation

Go to your home directory on your EC2 machine, /root:

%% cd

Grab the source file:

%% curl -O http://angus.ged.msu.edu.s3.amazonaws.com/bwa-0.5.7.tar.bz2

Unpack it, using ‘j’ instead of ‘z’ because it’s a .bz2 file:

%% tar xjf bwa-0.5.7.tar.bz2

Compile it:

%% cd bwa-0.5.7
%% make

Install the new ‘bwa’ program into /usr/local/bin:

%% cp bwa /usr/local/bin

Now, go to your data directory. I’ll assume you’re using the Campylobacter 1m read dataset from Mapping with bowtie:

%% cd /mnt/campy

Index the reference genome:

%% bwa index -a is campy.fa

Note: for reference databases bigger than 10mb, you need to use ‘-a bwtsw’; for databases smaller than 10mb, you need to use ‘-a is’, as per the bwa man page.

And generate a mapping of all the reads:

%% bwa aln campy.fa campy-pre-1m.fastq > campy-pre-1m.bwa.sai

This may take a few minutes. You can speed it up on a two-core machine by specifying ‘-t 2’ (to use two threads).

This ‘sai’ file is a binary file that you can’t look at with ‘less’. You have to convert it to a SAM file:

%% bwa samse campy.fa campy-pre-1m.bwa.sai campy-pre-1m.fastq > campy-pre-1m.bwa.sam

and finally, this SAM file can be viewed or interrogated using samtools (see Visualizing mappings with Samtools). To do this, first make sure that you’ve indexed ‘campy.fa’ with samtools:

%% samtools faidx campy.fa

Now, convert the .sam file into a .bam file:

%% samtools import campy.fa.fai campy-pre-1m.bwa.sam campy-pre-1m.bwa.bam

Sort it:

%% samtools sort campy-pre-1m.bwa.bam campy-pre-1m.bwa.sorted

Index it:

%% samtools index campy-pre-1m.bwa.sorted.bam

...and now you can do all the other things that samtools lets you do, such as retrieve mappings to specific intervals,

%% samtools view campy-pre-1m.bwa.sorted.bam 'campy_genome:1-25'

or look at it with tview:

%% samtools tview campy-pre-1m.bwa.sorted.bam

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