How To Align 15Bp Length Reads By Shrimp

Question

[Yunfei Li]

Hi, I am testing different aligners for mapping single-end 15bp length reads back to genome. For SHRiMP, What would be an appropriate parameter setting? The parameter system seems much more complicated than other aligner like bowtie, bwa.

Answer 1

[Stevelor]

Have you seen this?? Haven't found anything else about 15bp reads :(

[Yunfei Li]

thanks, I test bowtie and BWA, bowtie looks a bit better for me