Hi all, I have a weird situation here: I am working with archaic DNA (aDNA) reads, and we had a few sequencing run in the past weeks. The cycle number was set to 50-100 (each run had its own cycle number), but some of the samples were the same (in this case I merged the fastq files to a single R1 and R2 file/sample). Therefore I had fastq files with different read lengths, where the reads' are paired end, or just because of the aDNA length variation are the same in the R1 and R2 file. When I used BWA to align reads to reference as PE reads, the results were terrific (the mismatch rate and read-position shifting in spec. regions were enormous). When I tried to cat the barcode/adapter trimmed fastq files and treat them as SE reads, I have got a very nice alignment with a correct coverage (however the MapDamage results were not that nice-looking, but it was slightly okay). My problem is that besides the good-looking results, I am not sure that my approach is flawless or even acceptable, so I just need some comment/advice about it. Thanks in advance!
PS.: I did not use merging, because it eliminates a considerable amount of reads (10-50%).