What it does

Trims specified number of characters from a dataset or its field (if dataset is tab-delimited).

Example 1

Trimming this dataset:

1234567890
abcdefghijk

by setting Trim from the beginning to this position to 2 and Remove everything from this position to the end to 6 will produce:

23456
bcdef

Eaxmple 2

Trimming column 2 of this dataset:

bcde  12345   fghij   67890
fghij 67890   abcde   12345

by setting Trim content of this column only to 2, Trim from the beginning to this position to 2, and Remove everything from this position to the end to 4 will produce:

abcde  234     fghij   67890
fghij  789     abcde   12345

Trimming FASTQ datasets

This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected Yes from the Is input dataset in fastq format? dropdown. If set to Yes, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset:

@081017-and-081020:1:1:1715:1759
GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
+
II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B

cab done by setting Remove everything from this position to the end to 31:

@081017-and-081020:1:1:1715:1759
GGACTCAGATAGTAATCCACGCTCCTTTAAA
+
II#IIIIIII$5+.(9IIIIIII$%*$G$A3

Note that headers are skipped.

WARNING: This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example.