Happy New Year,
I have a question regarding BWA (this is my first time doing it). I have a nice working script for paired-end reads. However, when I converted my SRA files to Fastq, I used fastq-dump --split-3, because I am also interested in small reads due to the quality of DNA I am working on now.
- Fastq generated three files fastq, fastq_1, fastq_2. Is it possible to put all three to bwa mem? Or what is the best strategy in this case?
- I have some files which are single reads. Can I use BWA MEM for single reads too (quality of DNA is low meaning I have more short reads than long, and the longest is about 100 bp)?