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doc:trim

Trim

Tool version

0.0.1

Keywords

Remove, Beginning / Head, End / Tail, Lines, FastQ, Substring

Summary

Trims specified number of characters from a dataset.

Description

This tools deletes a specified number of characters from the ends of a dataset. If the dataset is tab-delimited it is possible to trim only a specific column of the dataset.

General comments (Warning/Tips)

This tool is able to trim sequences and quality strings in fastQ format.

Check that the input dataset is formatted as follow:

  1. each read and quality string occupy one line
  2. '@' (read header) and “+” (quality header) lines are evenly numbered. (In Galaxy, numbering starts at 0.)

Input

  • this dataset: select the input file.
  • Trim this column only: if the file is tab-delimited, you may choose to trim only one column. Columns are referenced with integers ( 1 corresponds to the first column ).
  • Trim from the beginning up to this position: every character located before this position will be deleted.
  • Remove everything from this position to the end: the position you indicate will be kept and everything located from this position to the end will be removed.
  • Is input dataset in fastq format?: if yes, only the reads and quality strings will be trimmed. The headers will be preserved.
  • Ignore lines beginning with these characters: 16 options are available. Depending on the format of your dataset you may select one or several.

Output

The output dataset corresponds to the trimmed input dataset. Both have the same format.

Example

Usage Example: trimming poor quality or ambiguous data. Most of the time these data are located close to the end of the fragments.

Input

this dataset: file_trim.txt

Trim this column only: 0

Trim from the beginning up to this position: 3

Remove everything from this position to the end: 40

Is input dataset in fastq format?: yes

Ignore lines beginning with these characters: Unselect all

With file_trim.txt containing:

Output

Only the sequence and quality lines are trimmed.

Edited on

July 16th, 2014

doc/trim.txt · Last modified: 2014/11/28 17:02 by slegras