Trimming FASTQ files using Trimmomatic

Question

[Researcher]

I have paired read FATSQ files and I am trying to follow the instructions in the paper that generated these files and the paper says reads were simply trimmed to 28 bp. The problem is if I run Trimmomatic by setting MINLEN to 28 the first read file already has reads below 28 bp but the other one has reads around the range of 57 and only the first 8 nucleotides are meaningful while the rest are basically the poly A tail so it will still end up with lots of polyA tails. What exactly am I supposed to do, am I doing the correct thing here?

[ATpoint]

I cannot comment on a paper without a link, but in general, if you simply want to trim to a fixed size you do not need trimmomatic and can simply use lightweight tools such as seqtk trimfq to make fastq files with a fixed read length. https://github.com/lh3/seqtk

For more help one would need to know what data that is.