Bowtie2 reference genome

Question

[Ada]

When you map reads (.fastq) against a large genome database (indexed creating bowtie2) of a particular species, does Bowtie2 mapping show you which particular reference genome closely aligned to the input paired reads?

[GenoMax]

does Bowtie2 mapping show you which particular reference genome closely aligned to the input paired reads?

Is that not the reason one does mapping to a reference in first place?

a large genome database

What do you mean by that? Something that has more than one reference (e.g. more than one bacterial genome or more than one chromosome for a single genome)?

[Ada]

Essentially, something that has more than one reference.

[Ada]

Essentially, would bowtie2 show you the most closely aligned from an index with multiple reference genomes of the same bacterial species?

[GenoMax]

It may not since once a read starts multi-mapping it would become subject to limits for those. If you allowed no mismatches then your search may become very strict but unless you allow mismatches you will not find hits to related genomes (which may have one or more mismatches).

Your better bet may be to try bbsplit.sh from BBMap suite which allows you to map/bin the reads against multiple genomes at the same time. You can then see if a read multimaps within and/or across genomes and decide how to handle it (look at the ambiguous= and ambiguous2= parameters.

If these are closely related genomes then aligners are going to have a hard time discriminating with short read data.

[Ada]

Thank you for letting me know. That makes sense.