Groomer vs datatype

Question: Groomer vs datatype

2.5 years ago by

France

devillartay • 30 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

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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by devillartay • 30

2.5 years ago by

bryantl • 90

United States

bryantl • 90 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 COMMENT • link written 2.5 years ago by bryantl • 90

2.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

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