Hi All,
After I use fastp to preprocess the reads, the fastqc report became worse. It seems that the reads have been preprocessed since the fastqc report of the reads I obtained showed adapter content = 0. Is that the case? But why this would happen when doing pre-processing one more time and the quality becomes worse? Should I use the reads after fastp or use the reads before fastp? Any help would be appreciated!
Before fastp:
after fastp:
And this is the screenshot of fastp report below
1 answer
the fastqc report became worse
I don't see a lot of difference above. It is not necessary that your data have adapter sequences. It appears to have some adapters. Because you have a set of reads that were trimmed, you now see a tail on the left side of the plot with majority of sequences still being full length i.e. 150 bp (sharp peak). Previously they were all 150 bp so that is why FastQC plotted that weird triangle like thing.
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