I need some help. I am trying to map two fastq datasets with Bwa-mem. If I design a workflow by: Input dataset > FastQC > BWA-Mem, then just selecting the two raw fastq data and I am able to run and get the FastQC data and BWA results successful, with the default. However, If I run step-by-step to (1)FastQC, (2) BWA, I cannot select input dataset in BWA since it said there is no fastqsanger file available from the pull-down thus unable to run the BWA. Furthermore, If I manually change the datatype of FastQC's output's rawdata from txt to fastsanger (since the webpage of FastQC result shows good score and Pass QC), the BWA-MEM page shows the list of selection of input dataset is "Fastqc on data ..." (fastsanger)" but not my raw data Fastq file, but running the BWA will be unsuccessful with fatal code and exit.
Can anyone help to explain this and guide me to go through ? Thanks.
Both answers below are correct. Here is how to determine which to use is appropriate for your data (includes video): https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA