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Old 11-13-2013, 03:22 AM   #1
Junior Member
Location: CAU,Beijing,China

Join Date: Mar 2013
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Default how to set parameters for mapping reads to a bacterial genome using "bwa-mem/bowtie"?

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?
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Old 11-13-2013, 03:54 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

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

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