by columnfastq_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'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.