How to input a single paired-paired in data file into Trimmomatic? How to split forward and reverse reads of different length?

Hi, I have a fastqsanger.gz paired-end data file with both forward and reverse reads combined into a single file. I want to use Trimmomatic to trim adapters and set a quality score. I don’t see an option to input a single paired-end file. Would it be advisable to input this as a single-end file instead?

I was originally going to use FASTQ Splitter to first split the data into two separate files for the forward and reverse reads, however my forward and reverse reads are not all the same length which is required for this tool. Also there is variable length for each read.

I am new to this so I’d really appreciate any help, thank you! :smile:

I figured I’d give an update in case this helps someone else in the future.

I reimported my data which was on NCBI using the tool “NCBI using Faster Download and Extract Reads in FASTQ”. This imported my pair-end data into a separate file for the forward and reverse reads and eliminated needing to use FASTQ Splitter. I was then able to use Trimmomatic with the paired-end setting with my two files.