RMAP was developed for Solexa reads.

TIP. The tool will guess the length of the reads, however, if you select to trim the reads, the Reads length must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end.

What it does

This tool runs rmap (for more information, please see the reference below), mapping Solexa reads onto a genome build.

Parameters

• Minimal Length of a Hit (-h) : this is the seed length or the minimal exact match length
• Number of Mismatches Allowed (-m) : the maximal number of mismatches allowed in an alignment
• Read Length (-w) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.

Reference

RMAP is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/