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SOAP denovo trans

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

soap-denovo-trans rna-seq next-gen
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updated by Ram Ram • written by Rahul • Rahul

1 answer

My transcriptome assembly reported it to be 1.6

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written by kanika.151 kanika.151

Could you show how your config_file looks like?

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written by kanika.151 kanika.151

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

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updated by Ram Ram • written by Rahul • Rahul

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

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written by kanika.151 kanika.151 
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
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updated by Ram Ram • written by Rahul • Rahul

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