User: lamz138138

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lamz1381380
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Posts by lamz138138

<prev • 8 results • page 1 of 1 • next >
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Is it possible to get trace and pulse files?
... Hi! I had processed with h5 files to find base modification recently, and I think the raw information in trc.h5 and pls.h5 files may give me more useful information, so I want to know is it possible to get these two files? If I can get it, how should I do? Also, would any adverse effect for downstr ...
pulse pacbio sequencing written 11 months ago by lamz1381380
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Comment: C: Why we need 100X coverage to get a high-quality assembly?
... Hi, sorry for the delay reply! In fact, I had used BBMap to produce my short reads and it is very useful for me to evaluate the assembly effect. Also, thanks for all suggestions. Best wishes! ...
written 11 months ago by lamz1381380
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Comment: C: Why we need 100X coverage to get a high-quality assembly?
... Hi, Brian Bushnell, thanks for reply! Could you explain 20X is only 10X per ploidy more? In my opinion, it would reverse the sequence to get the overlap between reads, then correct them, so the dipliod wouldn't influence the effect of correction. But in the final step, dipliod would result in alter ...
written 11 months ago by lamz1381380
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Comment: C: Why we need 100X coverage to get a high-quality assembly?
... Hi, thanks for your reply again! According to the menu of CANU, I think we need more than 30X data to get the 20X correted data. All together, it seemed we couldn't know whether we can get a better genome before assembly with real data.Maybe I could sequence 20X data then assembly with different to ...
written 11 months ago by lamz1381380
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Comment: C: Why we need 100X coverage to get a high-quality assembly?
... Hi, Medhat! Thank you for your reply. I am planning to assembly human-related species, but with 100X pacbio data is too expensive, so I wondering whether lower coverage is possible. However, according to the recently paper of human, gorilla, they all 100X data, and further integrated with BioNano a ...
written 11 months ago by lamz1381380
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Why we need 100X coverage to get a high-quality assembly?
... Hi! When performing genome assembly, it usually need high coverage data, such as more than 50X for pacbio, in my opinion, 10X would be enough to correct the high-error reads and assembly the genome. Considering we can't get the uniform coverage across the genome, thus we increase the total coverage ...
genome assembly coverage pacbio written 11 months ago by lamz1381380
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How to detection segmental duplications?
... Hi! I am interesting in segmental duplications detection after *de novo* genome assembly. After review several papers, there are some softwares could be annotated segmental duplications, and they were rely on previously library, or need next-generation sequencing data. It seemed only whole-genome ...
genome assembly alignment written 14 months ago by lamz1381380 • updated 14 months ago by WouterDeCoster23k
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Answer: A: SOAPdenovo2 contig error
... Hi! I had the same problem, did you solve it? With subset of reads, no error was reported, so I thought it may out of memory. After tracing the memory usage, I exclude this possibility. Any suggestion would be grateful! Following is my log: 41306549 none-palindrome edge(s) swapped, 0 palindrome e ...
written 19 months ago by lamz1381380

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