To find the correct paramter

Question

[bandanaschapagain]

Hi All, I am new in understanding the software manuals. So, I need a help in the matter which may be very simple to most of you.I am trying to align my viral reads data to the viral reference genome. I am using bowtie for my analysis. Using bowtie, I used the default parameters. I am trying to do a very strict alignment analysis like not allowing mis-match and insertions. That means to have the result as the end to end match. In that case,which parameters do I have to focous on?

Regards, Bandana

[GenoMax]

Rewriting the title of this post would clarify what the question is about.

I assume you are referring to bowtie v.1 (since you are referring to end-to-end match). I generally find bbmap options easier to understand. See this to help with your question: C: bwa mem perfectly align reads over their entire length

[WouterDeCoster]

In addition to rewriting the title to better reflect the content of the question, as suggested by genomax2, it would be a good idea to chose accurate tags for your question. You added blast and rna-seq, but both are not discussed in your question (although it can still be about RNA-seq, we don't know that)

Answer 1

[Sinji]

You may want to give teaser a try. Teaser is a mapping performance analysis software. You can run multiple mappers on your dataset or stimulated datasets with different combinations of parameters and see which ones will give you the the strictest alignments. Fast, and very helpful for this sort of thing.