how to set parameters for mapping reads to a bacterial genome using "bwa-mem/bowtie"？

[joyjane88]

Hellow everyone,

Now, I'm trying to map a set of illumima RNA-seq data to the reference genome(a bacterial one). My data sets are PE type and have been cleaned and trimmed with a readlength 90nt. I am wondering how to set parameters for mapping reads to a bacterial genome using "bwa-mem/bowtie"？Someone told me that the default parameters is OK. Would someone just tell me which options are necessary to be specified and how?

[dpryan]

As a general rule, try a new program with the default options first. In this case, the defaults will probably work fine.