Can trimmomatic be used on paired interleaved fastq files?

[reliscu]

Apologies for the simple question, but I can't seem to find a straight forward answer searching online.

I created interleaved fastq files for each of my libraries, and was going to proceed with trimmomatic.

I had intended to use the the PE flag, but it occurs to me that I would be feed in just one file per sample. Would this trip up trimmomatic? In other words, do paired end files need to be separated, or can trimmomatic detect interleaved files?

Thanks in advance!

[GenoMax]

Very few tools understand interleaved data files. I don't think trimmomatic is one of those tools. You can "cat" your file pieces for R1/R2 reads together like I showed you in other thread. Then use the 2 files as input to trimmomatic.

[reliscu]

Thanks for your quick response! Very helpful.