Question: FastQC form setting and usage
gravatar for ginna
4.2 years ago by
United States
ginna0 wrote:

What does Contaminant list mean? For an example when I select the settings for the FastQC:Read QC tool there is a drop down box and my reference genome is listed there. Should I select it?

forms manuals usage fastqc tools • 1.7k views
ADD COMMENTlink modified 4.2 years ago by fubar1.1k • written 4.2 years ago by ginna0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The FastQC manual is linked from the tool form, which is the best source for usage details.

However, I can let you know what I have used this for: screening out known artifact from the analysis. For example, if in a public dataset an earlier run of FastQC revealed an overrepresented sequence that was identified as likely being an adaptor, or if the description of the data contains an adaptor. Use a tabular formatted file: column 1 an identifier, column 2 a nucleotide string. The underlying tool may also accept a fasta file, but not in the Galaxy wrapped version, that I know of.

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Jennifer Hillman Jackson25k
gravatar for fubar
4.2 years ago by
fubar1.1k wrote:

The help text on the tool form is about all you'll find anywhere but an example with some explanation is here:

The choices you see in the fastqc tool are the tabular datasetsl from your local history as defined by the tool xml:

 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list" 
           help="tab delimited file with 2 columns: name and sequence.  For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/>

Choosing the reference genome as the contaminant sequences list would probably be a very bad idea :)


ADD COMMENTlink written 4.2 years ago by fubar1.1k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 177 users visited in the last hour