Does Trimmomatic merge paired-end reads into "single-end" files?

Question

[smo]

I'm new to NGS analysis, and I'm trying to build a de novo assembly from paired end sequencing data (150-bp paired end reads; RADseq libraries from insects). My reads have been demultiplexed according to the individual specimen they came from (70 specimens total) and are provided as separate paired end files (R1 and R2). My issue is that Trimmomatic seems to combine these into a single file for paired reads. What impact does this have on downstream analysis, if any? Should I treat the 'forward_paired' output file as single end data? Do I lose information if I proceed as if I have "single end" input?

The assembler I want to use is MaSuRCA (can't seem to get SOAPdenovo to run on my computing cluster), but it requires separate R1 and R2 files for paired end data, and I don't think I can restore those from the Trimmomatic output. Specifically, the 'forward_paired' output files do not seem to contain any reads labeled as R2 - all the reads show a '1' where the '2' would be.

Any insight on this would be very welcome, thank you!

EDIT: OK, I'm an idiot. The R2 files are output as the "reverse_paired" file. The specific use of the words "forward/reverse" and "paired/unpaired" had me confused - implying that the 'paired' files contain interleaved reads, and that the 'reverse_paired' files provides the reverse complement of the 'forward_paired' (although in practice this would never be necessary'.

So the short answer to my question is, no, Trimmomatic does not output interleaved reads.

[MiladAD]

Hi friend, your explanation isn't clear. do you have single end file from paired end sequencing? and you want to make forward and reverse files from that?

for this question: "Do I lose information if I proceed as if I have "single end" input?" absolutely yes, you will lose important information which can make your assembly more confident at the downstream analysis.

[smo]

Sorry, I was confused by the default naming of Trimmomatic's output files. I do indeed have separate R1 and R2 files as output! All is well.

[cpad0112]

My issue is that Trimmomatic seems to combine these into a single file for paired reads. 

what is the command you used in trimming PE files?

[smo]

I'm using the PE command. Turns out I just badly misunderstood the output files.

[cpad0112]

Good that things are working now. Good luck with rest of the workflow.