bowtie for short reads

[alessandromacc]

Dear developers,

I am currently working with miRNA-seq reads from Illumina platforms, whose length ranges roughly from 16 to 30 nucleotides.

Do you think bowtie can outperform other popular mappers such as BWA, when it come to mapping these very short reads?

I am mapping these short reads on the reference miRNA database (much shorter than the whole reference genome). What alignment mode (-n or -v) would you suggest in this case? Or would you suggest to use the default parameters?

Thank you kindly!

[mschilli87]

@alessandromacc: You might want to have a look at miRDeep2 which was developed specifically to predict and quantify(!) (animal) miRNAs and relies on bowtie for mapping of sRNA-seq reads.

Disclaimer: I am a contributor to miRDeep2, though not involved in the original publication.