Question: Switching from fastq to fastqsanger?
0
gravatar for luca.marisaldi
9 months ago by
luca.marisaldi30 wrote:

Hello everyone! I am going to analyze data coming from the Illumina HiSeq 3000 system. The datatype of my raw data is .fastq and Galaxy has correctly recognized them.

As I need to run Trimmomatic on Galaxy I noticed that the datatype must be .fastqsanger, therefore I should change to this kind of format in order to perform the analysis. Fastq Groomer seems to be suitable for that but looking on some posts/documents maybe could be an unnecessary step because if I understood well the latest Illumina encoding is already "sanger".

My questions are:

  • Is the extension of these files just a question of formality? In this case I would just change "manually" the datatype from fastq to fastqsanger.
  • Or using Fastq Groomer is still a necessary step to switch between them?

Thank you in advance!

Luca

ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson23k • written 9 months ago by luca.marisaldi30
1
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

You are correct - the names/extensions on dataset names do not matter. The metadata assigned to the datasets is the part that needs to be changed.

Click on the pencil icon to reassign the datatype for data that is already loaded.

If you are not 100% certain the data is already in fastqsanger format, this is how to check: https://galaxyproject.org/support/fastqsanger/

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson23k
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