Question: Groomer vs datatype
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gravatar for devillartay
18 months ago by
devillartay30
France
devillartay30 wrote:

Hello all, I've a naive question: fastq file have to be modified to fastqsanger format before running galaxy tools. I see to ways to do it: 1) change manually the datatype -----> it takes no time 2) use fastq grommer -------> it takes ages !!! Beside the fact that groomer has to be used in workflows (if format change is necessary) is there any reason to use it instead of changing datatype manually in other cases? Thanks jp

galaxy • 354 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson23k • written 18 months ago by devillartay30
0
gravatar for bryantl
18 months ago by
bryantl90
United States
bryantl90 wrote:

You should use the groomer if you are not 100% sure that your files are in fastqsanger format. If you know that for sure (in your case you already modified them) changing it manually is more efficient.

ADD COMMENTlink written 18 months ago by bryantl90
0
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Here is how to check the type. From the information, you can determine what settings to use with the Fastq Groomer tool (if needed) or if the type can just be assigned. Using the wrong quality score scaling will negatively impact an analysis, making it unusable. https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Tip: To save time, the first 100 or so sequences from any large fastq file can be used with FastQC to determine the original datatype - no need to process the entire file at this point. (Select first lines from a dataset - enter the number of lines as a multiple of 4, since there are 4 lines per fastq sequence).

Best, Jen, Galaxy team

ADD COMMENTlink modified 18 months ago • written 18 months ago by Jennifer Hillman Jackson23k
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