Question: How to decide Gap/mismatch penalties ?
gravatar for KVC_bioinfo
2.5 years ago by
KVC_bioinfo410 wrote:


I am a new student of Bioinformatics. I am trying to learn how to set optimal the gap or mismatch penalties for aligning the reads. So, If I am trying to align the reads(RNA-seq) How to decide what is the best gap penalty or what is the best mismatch penalty? particularly while using bowtie2.

Thank you in advance.

#gappenalty #bowtie2 • 1.3k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 2.5 years ago by KVC_bioinfo410
gravatar for Devon Ryan
2.5 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

Firstly, don't use bowtie2 for spliced data.

Secondly, use the defaults. As a rule of thumb, always use the defaults with tools unless you have a good reason to do otherwise (the exception is the number of threads to use). It's generally the case that the person who wrote a tool put more thought into the various implications of the settings than you'll want to. Have a look at the results and judge then if some of the settings need to be tweaked.

ADD COMMENTlink written 2.5 years ago by Devon Ryan94k

I am aligning it to reference transcriptome.

ADD REPLYlink written 2.5 years ago by KVC_bioinfo410
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