I did a smallRNA-Seq experiment where the sequencing provider was supposed to sequence small RNAs 15-25 nt. After trimming adapters, I see that there are reads ranging in size from 15 to 35 bp, but also reads that are 50 bp (the full length of the read). Since I sent total RNA, I assume the 50bp are RNA species other than miRNA/smallRNA. I was to extract all reads <40bp and >49bp in 2 separate files.
The only way I can figure to do this is to convert to fasta, determine the length of each read using a tool, use R to create my 2 lists of reads based on sizes, save the list and use seqtk to extract from fastq. This sounds long and silly.