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. 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 firstname.lastname@example.org Thanks a lot!"