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How to decide Gap/mismatch penalties ?

Hello,

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.

bowtie2 gap-penalty
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updated by Ram Ram • written by KVC_bioinfo KVC_bioinfo

1 answer

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.

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written by Devon Ryan Devon Ryan

I am aligning it to reference transcriptome.

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written by KVC_bioinfo KVC_bioinfo

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