Who can give a finally determined answer:  **what is paired and unpaired reads by trimmomatic**? what kind of sequences are in unpaired reads? please see [the question link and my comments][1]. Many many many thanks! here is my comments:

 

> "Hi Genomax, I see your reply for this question, but I still do not
> understand what is unpaired reads or unpaired.fastq file? based on
> your answer, my understanding is that for a Paired End sequencing,
> generally, the types of sequences in the R1 file is equal to that in
> the R2 file. Here, we do not care about the number of each sequence.
> for instance, if one sequence cannot pass the QC (set in
> trimmomatic)in R1 file, but this sequence pass the QC in R2 file,
> however, this sequence in both R1 and R2 file will be classified into
> unpaired reads/.fastq file, which means all the copies in R1 and R2
> files also will be classified into the unpaired reads. Or another
> understanding is that one sequence exist in both R1 and R2 file, but
> one copy in either R1 or R2 cannot pass the QC, this copy will be
> classified into unpaired fastq file/reads. (I think the second view
> might right). if so, some guys also mentioned using the unpaired for
> alignment/mapping with BWA, whether these under-QC sequences should be
> dealt with trimmomatic again with a strict set? are they useful?
> Finally, what kind of sequences are in unpaired.fastq file? please
> five some examples. my email is wangqk198738@163.com Thanks a lot!"


  [1]: https://www.biostars.org/p/192788/
> my understanding is that for a Paired End sequencing, generally, the
> types of sequences in the R1 file is equal to that in the R2 file.

I don't know what you mean by that. There should only be one type/format of sequences, fastq.  Number of reads in `R1/R2` files will be identical when the sequence comes off the sequencer.

> Here, we do not care about the number of each sequence.

Some may not (if you are willing to accept files that are out of sync in terms of order of `R1/R2` reads. Aligners will produce odd results if you use such a file.

> if one sequence cannot pass the QC (set in trimmomatic)in R1 file, but
> this sequence pass the QC in R2 file, however, this sequence in both
> R1 and R2 file will be classified into unpaired reads/.fastq file,
> which means all the copies in R1 and R2 files also will be classified
> into the unpaired reads.

That is the reason you should trim reads together and use a trimming program that is PE aware. There should be only one copy of sequence for each cluster coordinate.

