Question: How to set parameters for SOAPdenovo-Trans
0
gravatar for Rahul
3.1 years ago by
Rahul30
India
Rahul30 wrote:

Hello,

I am facing some problems in understanding of parameters given in APPENDIX A: example.config on SOAPdenovo-Trans site (http://soap.genomics.org.cn/SOAPdenovo-Trans.html). I have converted one SRA file to Fastq format (http://www.ncbi.nlm.nih.gov/sra/SRX099032[accn]). 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 weather (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

 

 

 

 

 

ADD COMMENTlink modified 3.1 years ago by rtliu2.0k • written 3.1 years ago by Rahul30
1
gravatar for rtliu
3.1 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

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

ADD COMMENTlink written 3.1 years ago by rtliu2.0k

Thank you very much for your suggestion..

ADD REPLYlink written 3.1 years ago by Rahul30
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