Tool usage fastq-join

Hello, there all
While I am new to galaxy, I have a basic query
After uploading my datasets, I joined the paired end data by using fastq-join, with each read about 4.8 gb in size
It produced three different files as
1 fastq-join on data 27( unmatched 2) ( size 4.6 gb)
2. Fastq-join on data 27 ( unmatched 1 ) size 4.6gb
3. Fastq-join on data 27 ( joined) size 210.4 mb
Now my question is which file I have to choose for further downstream analysis.
Thanks in advances
Any possible help highly appriciated

Why in particular are you using fastq-join? This joins reads only when they are overlapping, and most fastq reads will not overlap. From the size of your outputs it certainly looks like you have non-overlapping reads. Depending on what you are trying to achieve, you will either use the two read datasets (which here are largely preserved in the “unmatched 1” and “unmatched 2” datasets or you will use the joined one (but this seems very small in your example).

If you explain a bit more about the analysis you are trying to do it will help people advise better.

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