What is the best way to map/align my reads on a given genome? I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the two, therefore I wonder what is the best tool to do this? I have single-end reads.
What I need is to have a percentage of uniquely mapped fragments, mapped to multiple loci and, say, unmapped. Can bowtie do the job? Is there a standard explanation procedure explained elsewhere? Thanks.
This is a pretty straightforward analysis, assuming that you want to measure something like &quot;how many reads align to genome 1, and how many reads align to genome 2?&quot;.

The bowtie2 manual has a section on this.
There are other tutorials for bowtie2.
bwa is also well-suited to this task.

You should be able to then use samtools to compute statistics on your alignments.