I want to align my samples by BWA. my samples are RNA-seq and Single-End. as I read on Manual Reference Pages - bwa (1), I have to run below command:
bwa mem [-aCHMpP] [-t nThreads] [-k minSeedLen] [-w bandWidth] [-d zDropoff] [-r seedSplitRatio] [-c maxOcc] [-A matchScore] [-B mmPenalty] [-O gapOpenPen] [-E gapExtPen] [-L clipPen] [-U unpairPen] [-R RGline] [-v verboseLevel] db.prefix reads.fq [mates.fq]
all arguments in [ ] are optional but my question is about "db.prefix" argument.I don't know what it is and how can provide it? based on alignment logic, it should be reference genome but I am not sure and if it is reference I don't know how to prepare it? I appreciate if you share your comment with me.
bwa is not an appropriate aligner for RNA-seq (unless it's prokaryotic), you should use a splice-aware aligner such as STAR or HISAT2.