How to decide Gap/mismatch penalties ?

Question

[KVC_bioinfo]

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.

Answer 1

[Devon Ryan]

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.

[KVC_bioinfo]

I am aligning it to reference transcriptome.