for Solexa Short Reads Alignment #if $trim.choice=="No": #rmap_wrapper.py $database $input_seq 0 $align_len $mismatch $output1 #else: #rmap_wrapper.py $database $input_seq $trim.read_len $align_len $mismatch $output1 #end if 0 1 3 5 No Yes rmap .. class:: warningmark RMAP 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 *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/