MULTIQC for miRNAseq data

Question

[Alana Conceição Maia Lessa]

Hello, I’m new to bioinformatics and need to preprocess microRNA sequencing data. This dataset (GSE166160) was the first one I chose to start the process. I started by generating reports with MultiQC, but I’m unsure how to interpret the results. When I click on an individual parameter (for example, in the first picture), the N content looks good. However, when I view all the parameters together (the images are from the same report), the N content is displayed in red (pic 2). I don’t understand why this is happening or how to proceed. I would greatly appreciate any help you could provide.!

Answer 1

[i.sudbery]

I wouldn't pay much attention to the "status checks" section of the report. The thresholds they use for various things are rather arbitrary, and may well not be suitable for the particular type of sequencing you are doing. Instead, examine each of the parameters your self and make your own judgements.