for Solexa Short Reads Alignment with Quality Scores #if $trim.choice=="No": #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len 0 $align_len $mismatch $output1 #else: #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len $trim.read_len $align_len $mismatch $output1 #end if 0 1 3 5 No Yes rmapq .. class:: warningmark RMAPQ was developed for **Solexa** reads. .. class:: infomark **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/