This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to Align to multiple reference genomes -> Discard multiply mapped reads?

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?

bwa cmd alignment
• 2,342 views • link
updated by h.mon h.mon • written by nattzy94 • nattzy94

1 answer

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

• 0 views • link
written by h.mon h.mon

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?

• 0 views • link
written by nattzy94 • nattzy94

Log in to answer this question.

More posts like this