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Background:
We performed NGS using cells collected from mice in a xenotransplantation study.
As such, the FASTQ files contain reads of DNA from both mice and human cells.
I expect ~30% of reads are contaminated by mice cells.
Question:
Is it wrong to directly align using the indexed human reference with bowtie2?
Is there a way to use two indexes at once with bowtie2? The goal here would be to get the % of reads that map to each genome.
I am not aware of a method using two indices in bowtie2 but here is a simple workaround:
Get human reference genome as fasta and suffix all fasta names with _human. Do the same with the mouse genome using _mouse. cat both together and build an index. Then you can later track back whether the alignment was done to human or mouse.
Edit: Be aware though that for those parts of the genomes that have high sequence similarity you will get multimapping reads with MAPQ of 0 (or at least very low).
