Bowtie database index question

[polsum]

Hi

I am trying to map illumina deepsequenced shortRNA transcripts to different types of RNA databases such as miRNA, piRNA, rRNA etc.

Is it a good idea to map the reads separately to each database or should I combine all the databases and create one index?

or should it really matter?

Thanks in advance.

[Ben Langmead]

Hi Polsum,

Besides convenience, the other major thing to consider whether/how you would like to consider repeats. Do you want to filter out repetitive evidence using the -m or -M options? If so, building all your databases into one index means that Bowtie is going to treat a single hit in more than one database as a repeat. Versus, if you indexed and queried each database separately, you would see the read yield unique hits in more than one database. Hope that makes sense,

Ben