Bowtie2 settings for human ribosomal DNA

[blancha]

Hi,

Any suggestions on modifications to make to the bowtie2 defaults settings to align ChIP-Seq data to human ribosomal DNA?

I've done the alignment with default settings to both the hg19 reference genome, and a FASTA file with only human ribosomal DNA.

The FASTA file is gi|555853|gb|U13369.1|HSU13369 Human ribosomal DNA complete repeating unit.

I'm now wondering if I should make adjustments to the settings for bowtie2 to take into account the specificities of human ribosomal DNA sequences, or if the default settings are fine.

Any suggestions or comments are welcome.

Thank you for your help,

Alexis