RMAPQ was developed for Solexa reads.

TIP. The tool will guess the length of the reads, however, if you select to trim the reads, the Maximal Length of the Reads 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 rmapq (for more information, please see the reference below), searching against a genome build with sequence qualities.

Parameters

• Minimal High-quality Bases (-M): the minimal length of the high quality score bases
• Minimum Score for High-quality Base (-q) : the minimal quality score
• Minimal Length of a Hit (-h) : the minimal length of an exact match or seed
• 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/