Basic reports
To generate a simple QC report, we call fastp and specify the location of our paired-end data:
The structure of the output is as follows:
First, there are stats about how many reads and bases are in your dataset before and after filtering is applied. Note that the R1 dataset decreases from 25,000 reads to 24,455—i.e. fastp removed 545 reads that it deemed low quality).
Next, you’ll see stats about how many reads and bases were removed and for what reason. For example, 942 reads were trimmed because adapter sequences were detected in those reads.
Although the report mentions reads being filtered, fastp does not overwrite your original data! Later in this tutorial, we’ll see how we can retrieve those filtered reads so we can use them in downstream analyses.