SOAP denovo trans

Question

[Rahul]

Hi,

I am using SOAP denovo trans for the analyzing RNA seq data. I have all prerequisite i.e parameter file etc...for the data analysis, but still following command is not working....

./SOAPdenovo-Trans all -s config_file -o outputGraph

Can anyone please help me to solve this problem.

regards
rahul

Answer 1

[kanika.151]

My transcriptome assembly reported it to be 1.6

[kanika.151]

Could you show how your config_file looks like?

[Rahul]

Thank you very much for your comment.

I have sorted out the problem. Could you please tell me what should be the ideal Average_number_of_contigs_per_scaffold for transcriptome assembly?

In my case, I am getting 1.0.

Regards
Rahul

[kanika.151]

I don't know how to get that number actually..

[Rahul]

max_rd_len=60
[LIB]
avg_ins=200
reverse_seq=0
asm_flags=3
rank=1
q1=SRR_1_fastq_quality_filter_out.fastq
q2=SRR_2_fastq_quality_filter_out.fastq
Kmer= 29
Assembler=31/127
Minimum conting for scaffolding=100