I am trying to create simulated Illumina reads using DWGSIM. I provided a fasta file (input.fa) and obtained the expected output with the command:
dwgsim -c 0 -C 30 -1 150 -2 150 -S 2 -Q 5
Using FastQC I obtained a decent quality score graph with well-spread bar plots, the only thing is that the average values are at 17 thus they look not good in a presentation: I, therefore, increase the average quality with the option -q using a phred33 code (B -> Q =33)
dwgsim -c 0 -C 30 -1 150 -2 150 -S 2 -q B -Q 5 <input.fa> <output>
but in this case the values had a single value of 2: then I used a phred64 code (a -> Q=33)
dwgsim -c 0 -C 30 -1 150 -2 150 -S 2 -q a -Q 5 <input.fa> <output>
in which case the values had a single value of 33: In both cases, though, there were no longer box and whiskers plots but a simple line (alas I don't know how to show the figure). I believe that DWGSIM and Fastqc use different phred codes, hence the downshift in the first plot; however I could not change the baseline coding for DWGSIM so that it could match Fastqc.
My questions are:
-q areturned the expected mean value of quality = 33 in the fastqc plot, I assume DWGSIM has the phred 64 score as default; it is possible to change the score to phred 33?
since the use of
-qhas removed the nice boxplots from the figure, it is possible to shift the boxplots to a given value? if not with the -q flag, maybe there is another way...?