How to Align to multiple reference genomes -> Discard multiply mapped reads?

Question

[nattzy94]

Hi,

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?

Answer 1

[h.mon]

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

[nattzy94]

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?