Nanopore data filtering using fastp

[emilydolivo97]

Hello, I'm running the following command in my terminal:

fastp -i user/nanopore/inputs/ -o user/nanopore/outputs/ -A -G --qualified_quality_phred 10 --reads_to_process 5000 --thread 8

Although I'm specifying the number of reads to keep as 5000, after running my pipeline, I find that my fastq files have different numbers of reads such as 4965, 4778, and 4653, but never exactly 5000. Does anyone have an idea on how to fix this problem, please?

[dsurujon]

Are the <5k read files the output before or after fastp processing? Could be that 5k reads were considered, but some failed QC and filtered out, and therefore didn't end up in your output fastq. If this is the case, you may want to process a larger pool, and then downsample to 5k