I have a fastq file from human data but we think when our colleague did sample prep, a mistake happened and now there is contamination with mouse sample. is there any quick way to understand if such a mistake happened (in addition to alignment to mouse and human separately)?
Example above removes reads that map to both genomes but you can take a look at ambiguous2= options if you want to to keep them.
ambiguous2=<best> Set behavior only for reads that map ambiguously to multiple different references.
Normal 'ambiguous=' controls behavior on all ambiguous reads;
Ambiguous2 excludes reads that map ambiguously within a single reference.
best (use the first best site)
toss (consider unmapped)
all (write a copy to the output for each reference to which it maps)
split (write a copy to the AMBIGUOUS_ output for each reference to which it maps)