How to set parameters for SOAPdenovo-Trans

Question

[Rahul]

Hello,

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.

Regards

rahul

Answer 1

[rtliu]

The above fastq data is paired-end, use SRA toolkit to get two fastq files SRR349653_1.fastq and SRR349653_2.fastq . e.g.

fastq-dump --split-3 SRR349653

Then set parameters for SOAPdenovo-Trans

#fastq file for read 1
q1=/path-to/SRR349653_1.fastq
#fastq file for read 2 always follows fastq file for read 1
q2=/path-to/SRR349653_2.fastq

[Rahul]

Thank you very much for your suggestion.