<p><strong>Background:</strong></p>
<p>We performed NGS using cells collected from mice in a xenotransplantation study.</p>
<p>As such, the FASTQ files contain reads of DNA from both mice and human cells.</p>
<p>I expect ~30% of reads are contaminated by mice cells.</p>
<p><strong>Question:</strong></p>
<p>Is it wrong to directly align using the indexed human reference with bowtie2?</p>
<p>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.</p>

<phylogenetics><bowtie2>
Bowtie2 mapping with multiple indexes
# Bowtie2 mapping with multiple indexes

(Asked by: username_0 on 2022-04-13)

**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.

**Tags:** phylogenetics, bowtie2

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## 0 answers

