I have 35bp Solid colorspace sequencing data, and the actual sequences to be mapped are 20-25bp after removing the linker sequence.
I hope to find all the hits allowing no more than n mismatches (say n=3), not only the best hit.
I know there is a -M option to specify -M sensitivity,35bp. I wonder whether this setting will guarantee the best sensitivity in this case. Since my reads are only 20-25bp long, should I changed the default 4 spaced seeds to 3?
I'm new to SHRiMP, so I'd like to hear some suggestions on setting the parameters of SHRiMP to achieve the best sensitivity.