Best aligner to identify single point mutation

Question

[silas008]

Hi, guys.

I am analysing some small RNAseq data. I saw possible alterarions in specific bases (normally one base per read) when I used Genome Browser to visualize the data. I mean, the reads aligned against the genome but I can see a mismatch in the same position for multiple reads in the same loci.

I was using bowtie for mapping, but I don't know if those alterations are real. What is the best aligner to identify those king of alterarions? And why it is the best one?

Thanks in advance

Answer 1

[ATpoint]

With these super-short reads you probably don't have much choice other than bowtie. I'd run it through a variant caller and see what comes out. Validate the mutation with Sanger if you can using genomic DNA.

[silas008]

Thank you very much.

Any suggestion of settings to make the mapping more accurated in this case?

[ATpoint]

Why not just using the defaults for now and see what the variant caller says, they do a lot of filtering internally towards base- and mapping quality.

[German.M.Demidov]

but this is RNAseq - maybe STAR/Kallisto/Salmon?

[GenoMax]

This is smallRNA seq as noted in original post.

[Hamid Ghaedi]

Kallisto and Salmon are kind of mapper not aligner. So cant be used for variant calling.

[German.M.Demidov]

Good points, thanks @genomax and @HamidGhaedi!