I am facing some problems in understanding of parameters given in APPENDIX A: example.config on SOAPdenovo-Trans site. I have converted one SRA file to Fastq format. After use of SRA toolkit I have got a single fastq file for paired reads. Now I am bit confuse about which parameter I should have to use whether (
p=/path/LIBNAMEA/pairs_in_one_file.fa) or (
q=/path/LIBNAMEA/fastq_read_single.fq). I would be very grateful if anyone could suggest me solution to get rid of this problem.