text: user7056: 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.
  
  user-1: 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).
  
original_text: 7056: <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>
   -1: <p>I am not aware of a method using two indices in <code>bowtie2</code> but here is a simple workaround:</p>
  <p>Get human reference genome as fasta and suffix all fasta names with <code>_human</code>. Do the same with the mouse genome using <code>_mouse</code>. <code>cat</code> both together and build an index. Then you can later track back whether the alignment was done to human or mouse.</p>
  <p>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).</p>
  