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
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