by column fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length' Absolute Values Percentage of Read Length int( float( value ) ) == float( value ) int( float( value ) ) == float( value )

This tool allows you to trim the ends of reads. You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer. For example, if you have a read of length 36:: @Some FASTQ Sanger Read CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA + =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ And you set absolute offsets of 2 and 9:: @Some FASTQ Sanger Read ATATGTNCTCACTGATAAGTGGATA + @.@;B-%?8>CBA@>7@7BBCA4-4 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: @Some FASTQ Sanger Read ATATGTNCTCACTGATAAGTGGATATN + @.@;B-%?8>CBA@>7@7BBCA4-48% ----- .. class:: warningmark Trimming a color space read will cause any adapter base to be lost.