Question

SOAP denovo trans

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9.1 years ago

Rahul ▴ 30

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 • 3.4k views

ADD COMMENT • link updated 2.4 years ago by Ram 44k • written 9.1 years ago by Rahul ▴ 30

Ram · Answer 1 · 2016-03-02

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8.7 years ago

kanika.151 ▴ 160

My transcriptome assembly reported it to be 1.6

ADD COMMENT • link 8.7 years ago by kanika.151 ▴ 160

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Could you show how your config_file looks like?

ADD REPLY • link 8.8 years ago by kanika.151 ▴ 160

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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

ADD REPLY • link updated 2.4 years ago by Ram 44k • written 8.8 years ago by Rahul ▴ 30

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

ADD REPLY • link 8.7 years ago by kanika.151 ▴ 160

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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

ADD REPLY • link updated 2.4 years ago by Ram 44k • written 8.7 years ago by Rahul ▴ 30