What it does

The readname produced by the "STR detection" step may contain spaces instead of underscores, which will cause downstream tools that use space as a column delimiter to fail. This tool will help convert space to underscore. If your input does not have spaces in readname column, this step can be skipped.

Citation

When you use this tool, please cite Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research

Input

The input files can be any tab delimited file.

If this tool is used in STR-FM for STRs profiling, it should be in the same format as output from STR detection program. This format contains length of repeat, length of left flanking region, length of right flanking region, repeat motif, hamming (editing) distance, read name, read sequence, read quality score

Output

The same as input format.