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Working with a new genome

In ncPRO-seq, it is possible to do small RNA profiling analyses in a new genome without giving any known annotations (miRNA, tRNA, etc). For example, you want to work in yeast. What you need to do is:

1. create the bowtie index of yeast genome with index name "yeast", put them in your Bowtie index folder
2. create a folder "yeast" in MY_INSTALLATION_DIR/annotation directory
3. create the "chrom.sizes" file of your yeast genome in MY_INSTALLATION_DIR/annotation/yeast folder. "chrom.sizes" is the reference idex file, which has two columns (name of chromosome and size of the chromosome) and can be generated using samtools