User: Yingzi Zhang

gravatar for Yingzi Zhang
Yingzi Zhang30
Reputation:
30
Status:
New User
Location:
Beijing
Last seen:
4 days, 10 hours ago
Joined:
1 month, 1 week ago
Email:
z******@yeah.net

Posts by Yingzi Zhang

<prev • 32 results • page 1 of 4 • next >
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Comment: C: task killed during SOAPdenovo's running
... They are multiple runs of the same library. I am not clear how to arrange runs in one or different library/libraries. And I am not clear how to set the option `rank =` neither. I will take your advice to estimate peak memory usage first. :) Thank you. Proof positively, I tried to ran the 7th librar ...
written 14 days ago by Yingzi Zhang30
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Comment: C: task killed during SOAPdenovo's running
... Yes i am the only user. I have about 400G reads in total. Did you have experience of how much memory I need? ...
written 14 days ago by Yingzi Zhang30
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Comment: C: task killed during SOAPdenovo's running
... RAM 768Gb; internal storage 50Tb ...
written 14 days ago by Yingzi Zhang30
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Comment: C: task killed during SOAPdenovo's running
... Yes. It's #config_file# max_rd_len=100 [LIB] avg_ins=469 reverse_seq=0 asm_flags=3 rank=1 map_len=32 q1=1_1.fastq q2=1_2.fastq [LIB] avg_ins=467 reverse_seq=0 asm_flags=3 rank=1 q1=2_1.fastq q2=2_2.fastq [LIB] avg_ins=474 ...
written 16 days ago by Yingzi Zhang30
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task killed during SOAPdenovo's running
... Hi all, I was running SOAPdenovo-127mer. The libraries are 12. When importing reads from the 7th library files, it reported that the task was killed and no more other information. Then I re-ran the same command and the task was killed again when importing the 7th library. How please? There was no on ...
software error assembly soapdenovo written 16 days ago by Yingzi Zhang30 • updated 14 days ago by Ram16k
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Comment: C: set "avg_ins" when using SOAPdenovo
... Got it. Thank you. Yingzi ...
written 18 days ago by Yingzi Zhang30
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Comment: C: still not clear about differences between de novo genome sequencing and genome r
... Many thanks. I feel no more self-doubt but full of strength! ...
written 18 days ago by Yingzi Zhang30
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set "avg_ins" when using SOAPdenovo
... Hi, all: I am using SOAPdenovo. When preparing config file, I need to set `avg_ins`. I know it means the average insert size of my library. I did insert size estimation. It reported like this: insert size (inside of regions) mean 57,532.59 standard deviation ...
assembly written 18 days ago by Yingzi Zhang30 • updated 18 days ago by genomax52k
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Comment: C: still not clear about differences between de novo genome sequencing and genome r
... There is a highly related genome accessible. I should try use it. I am only allowed to use data from the Internet, so no long reads till now (and I don't think there will be in a short time). Would the absence of long reads be fatal? Am I too confident with my 1T short reads?! ...
written 18 days ago by Yingzi Zhang30
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still not clear about differences between de novo genome sequencing and genome reseqencing
... Hi all, I am not clear about differences between de novo assembly and genome resequencing. I know that if there is no reference genome of the species I am interested in, I need to do de novo assembly to assemble and annotate the species. And if it is already assembled and annotated, I just ...
assembly sequencing written 18 days ago by Yingzi Zhang30 • updated 18 days ago by genomax52k

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