Question: bacteria genome mapping using bwa
gravatar for hirakuda
10 weeks ago by
hirakuda0 wrote:

Please someone suggest how to use bwa to map bacteria genomes to a sample? I want to use bwa mem. I did something bwa mem bacteria ref original sample > align.mem.out. and got some error. I dont know whether I am using it correctly. Can someone please suggest the correct command to use bwa to map severel bacteria together?

sequence genome • 122 views
ADD COMMENTlink written 10 weeks ago by hirakuda0

What is the error?

First you need to create an index for your bacterial genome reference.

Then you can align your sample(s) to the reference genome.

bwa index ref.fa

bwa mem ref.fa reads.fq > aln-se.sam

samtools view -S -b aln-se.sam > aln-se.bam

Note that the output format is not .out

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Fatima590
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