Parameter overview
Since the set-up and flow of parameters can be quite complex, there is a Parameter flow panel at the bottom of the configuration with a small graph for each parameter (see figure 7.9).
Figure 7.9: The reads parameter.
The reads parameter starts with user selecting data, and the sequences are exported in fasta format and used as input for the Bowtie script.
Figure 7.10 shows the max number of mismatches parameter which also starts with the user selecting a value that is passed to the Bowtie script.
Figure 7.10: The max number of mismatches parameter flow.
Figure 7.11 shows the reference seq parameter which also starts with the user selecting data which is passed on to the SAM/BAM import.
Figure 7.11: The reference seq parameter flow.