If we focus on, for example, the forward reads graph the bars between positions 20 and 100 are extremely short. You can see it if I amplify the image:
If I amplify the image more, in position 25 for example, you can see it better:
How I should interpretate the extremely short bars? Is it normal working with Illumina reads? Should I carry on with my analysis assuming that the sequences are OK?
Hi @dperez,
Yes this is perfectly normal for Illumina reads.
The quality plots you see here are a series of boxplots + whiskers beside each other. Since quality scores have a max, this means that when the median is very high (as is expected in 5’ of Illumina reads) the boxplot tends to look what you see with downward whiskers only.
You should carry on with your analysis, your quality plots look pretty decent!
