where to download (or how to build) bowtie index for mouse ribosomal rna

[joel.k]

Hi,

I want to find out how much (and also be able to filter at a later stage) data originating from ribosomal rna is in a fastq file (organism is mouse). I want to accomplish this by aligning the sample with bowtie1 against a bowtie index of mouse ribosomal rna.

I haven't been able to find this yet. Could someone please help point me in the right direction or guide me on how to use bowtie-build to construct an index (for which i'll also need help to locate appropriate source files)?

Thanks,
Joel.

[GenoMax]

You could visit:http://www.arb-silva.de/search/ Do a search for mouse and then download the sequence files as FASTA.

Then use the "bowtie-build" to create the indexes: http://bowtie-bio.sourceforge.net/ma...-build-indexer