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Best aligner to identify single point mutation

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

rna-seq
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written by silas008 silas008

1 answer

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.

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written by ATpoint ATpoint

Thank you very much.

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

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written by silas008 silas008

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.

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written by ATpoint ATpoint

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

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written by German.M.Demidov German.M.Demidov

This is smallRNA seq as noted in original post.

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written by GenoMax GenoMax

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

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written by Hamid Ghaedi Hamid Ghaedi

Good points, thanks @genomax and @HamidGhaedi!

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written by German.M.Demidov German.M.Demidov

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