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Hi, I try many different parameter K while using SOAPdenovo to assemble Streptomyces spp. genomes( 7-10M), but good results were still not got. The size of the genome in the result file(*.scafSeq) is about 2.8M at most. So now I don't know how to solve this problem?
Here is the configuration file I set up and the command to run it:
config.txt:
max_rd_len=150
[LIB]
avg_ins=409
reverse_seq=0
asm_flags=3
rd_len_cutoff=150
rank=1
pair_num_cutoff=3
map_len=32
q1=/apps/users/ziguang/Streptomyces/fastp/CYX02C3D3/CYX02C3D3.R1.fq.gz
q2=/apps/users/ziguang/Streptomyces/fastp/CYX02C3D3/CYX02C3D3.R2.fq.gz
run the command:
/usr/local/SOAPdenovo2/SOAPdenovo-63mer all -s CYX02C3D3.config.txt -K 45 -p 16 -R -o CYX02C3D3/result
Of course, I tried other values of K(23, 31, 35, 63......), but it didn't work.
The text was updated successfully, but these errors were encountered:
Hi, I try many different parameter K while using SOAPdenovo to assemble Streptomyces spp. genomes( 7-10M), but good results were still not got. The size of the genome in the result file(*.scafSeq) is about 2.8M at most. So now I don't know how to solve this problem?
Here is the configuration file I set up and the command to run it:
config.txt:
max_rd_len=150
[LIB]
avg_ins=409
reverse_seq=0
asm_flags=3
rd_len_cutoff=150
rank=1
pair_num_cutoff=3
map_len=32
q1=/apps/users/ziguang/Streptomyces/fastp/CYX02C3D3/CYX02C3D3.R1.fq.gz
q2=/apps/users/ziguang/Streptomyces/fastp/CYX02C3D3/CYX02C3D3.R2.fq.gz
run the command:
/usr/local/SOAPdenovo2/SOAPdenovo-63mer all -s CYX02C3D3.config.txt -K 45 -p 16 -R -o CYX02C3D3/result
Of course, I tried other values of K(23, 31, 35, 63......), but it didn't work.
The text was updated successfully, but these errors were encountered: