This is basic step to understand Galaxy and Galaxy workflow before we start RNASeq Analysis Lab exercise.Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).Its more important to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results.Here we are going to check the quality of given FASTQ file.
Here isthe sample FASTQ that we are going to use;
We can run above tools one by one and check the quality of the given FASTQ file but here we are going to merge all steps into one single workflow.
Once you logged into Galaxy, import input FASTQ file by clicking icon.Soon after,the asp5_leaf_read1.fq file available on your history.Then click the Workflow>Create new workflow.Now you can create the workflow similar to following image.You can do this by drag and drop tools in to workflow area and join each other using arrows.If you find It's difficult to create workflow, you can simply import the following workflow by clicking icon.
Now we can select asp5_leaf_read1.fq as input and run the workflow (Initial steps to RNASeq Analysis>Run).Here are the example results.
According to the box-plot graph manual.
According to the Nucleotide Distribution Plotter,The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem).