i am trying to generate simulated fastq files from a fasta reference using ART. Following the manual, I entered the following:
art_illumina -ss HS25 -i ./input.fa -p -l 50 -f 20 -m 200 -s 10 -o ./output
In this case, the simulated instruments is Illumina HiSeq2500, pair mates created, length 50 pb with mean of 200 (not sure what the difference is here) and a coverage of 20. I then checked the quality of the output with FastQC and I get reads of 50 bp in length but the quality is all skewed at the maximum of 38 quality: I therefore provided the values for maximum and minimum quality score:
art_illumina -ss HS25 -i ./input -p -l 36 -f 30 -m 50 -s 10 -qU 30 -qL 25 -o ./output
but in this case the quality score was not simply skewed: rather it was uniform with a single value of 30:
How can I obtain something more like the following plot? Thank you.