Question: How to Align to multiple reference genomes -> Discard multiply mapped reads?
gravatar for nattzy94
9 weeks ago by
nattzy9410 wrote:


I have reads containing E. coli, K. pneumoniae and GAPDH spike-in. I would like to align these reads to the 3 genomes and then discard reads that map to more than one of the references.

So far, I have concatenated all 3 fasta files into 1 composite genome. I have then used

bwa mem -c 1 <composite_genome.fasta> <Sample_x_R1> <Sample_x_R2>.

Can I check if this would be the correct way to do this or have I gone wrong somewhere?

cmd bwa alignment • 166 views
ADD COMMENTlink modified 9 weeks ago by h.mon25k • written 9 weeks ago by nattzy9410
gravatar for h.mon
9 weeks ago by
h.mon25k wrote:

BBSplit is a tool specifically designed with your goal in mind. See the tool announcement and the online documentation.

ADD COMMENTlink written 9 weeks ago by h.mon25k

Hey h.mon,

Thanks for the suggestion. I have used BBsplit to generate the fastq files that mapped to the corresponding genomes. Just to check, in order to get the number of mapped reads, do I just convert the .fastq files to .bam files and use samtools?

ADD REPLYlink written 9 weeks ago by nattzy9410
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