User: qiyunzhu

gravatar for qiyunzhu
qiyunzhu130
Reputation:
130
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United States
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http://qiyunzhu.blogsp...
Last seen:
3 months, 1 week ago
Joined:
5 years, 1 month ago
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Posts by qiyunzhu

<prev • 33 results • page 1 of 4 • next >
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Comment: C: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
... Thanks for your comment! Can you provide some examples (protein accession no.s) that result in "supplied id parameter is empty"? Let me see if I can fix it. ...
written 2.9 years ago by qiyunzhu130
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Comment: C: Find one taxonomy group best describing Blast hit table
... I see. Maybe I should design an algorithm myself... ...
written 3.2 years ago by qiyunzhu130
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Answer: A: A more robust tree viewer/editor than FigTree?
... [iTOL][1] is probably what you are looking for. [1]: http://itol.embl.de/ ...
written 3.2 years ago by qiyunzhu130
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Comment: C: Find one taxonomy group best describing Blast hit table
... Thanks for your comments. I understand and agree with your reasons. It's hard to statistically / automatically solve it though. For example, what if the top 10 hits are composed of 9 *Escherichia coli* and 1 *Salmonella*, with almost equally high bit score? Should I call it *E. coli* or Enterobacter ...
written 3.2 years ago by qiyunzhu130
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Find one taxonomy group best describing Blast hit table
... Dear community, I wish you all have a fruitful day. I am trying to answer this question: I have a sequence, and try to figure out what organism this sequence belong to. So I blast it, and obtain a list of Blast hits. The top 10 hits are from species a, with an average bit score = 500, followed up 2 ...
taxonomy blast written 3.2 years ago by qiyunzhu130
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Tool: SubDBer: Flexible taxonomy-based subsampling of sequence databases
... Dear community, I present SubDBer, a small program that allows users to build customized sequence databases that only include data of interest at designated comprehensiveness, based on resampling of large, standard databases. The sampling criteria are variable. For example, starting with NCBI nr, ...
subsampling genome database taxonomy blast tool written 4.3 years ago by qiyunzhu130
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Comment: C: choice of k-mer size for metagenomic assembly
... Thanks! They are paired end reads and are supposed to overlap (though not too many of them actually overlap well) I am trying to get something larger. What do you think I can do after assembly? E.g., I bin them by taxonomy and re-assemble within bins, using some more aggresive algorithms. Do you thi ...
written 4.3 years ago by qiyunzhu130
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choice of k-mer size for metagenomic assembly
... Dear community, I am doing de novo assembly of some metagenomic datasets. They are Illumina NextSeq reads (paired-end, 150 bp per read). I have tried IDBA-UD and SPAdes so far. Both of them gave me a final N50 values of some thousands, which is not too bad but still below my expectation. I noticed ...
genome assembly k-mer written 4.3 years ago by qiyunzhu130
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Answer: A: MrBayes chains converged, how to stop early?
... Ctrl + C will do the job. Then you need to manually add footers to the output files, *.t and *.p, to make them intact. Then you can go back to MrBayes and do sump. ...
written 4.3 years ago by qiyunzhu130
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COGsoft error can't open _hash.tmp
... Dear community, I wish you all enjoy this fantastic new year. I was recently trying out COGsoft (April 2012 release) to identify orthology in a bunch of proteomes. I precisely followed the instructions in the readme file, but when I was running COGlse, it says "Can't open input file ./data/tmp/_has ...
orthology cog blast written 4.6 years ago by qiyunzhu130 • updated 4.0 years ago by jk10

Latest awards to qiyunzhu

Popular Question 12 months ago, created a question with more than 1,000 views. For SubDBer: Flexible taxonomy-based subsampling of sequence databases
Popular Question 12 months ago, created a question with more than 1,000 views. For How to know if the third codon position is evolving too fast
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to know if the third codon position is evolving too fast
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to find a gene from genome shotgun reads
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Should I merge forward and reverse reads before mapping
Popular Question 3.2 years ago, created a question with more than 1,000 views. For choice of k-mer size for metagenomic assembly
Appreciated 3.4 years ago, created a post with more than 5 votes. For [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
Popular Question 3.5 years ago, created a question with more than 1,000 views. For [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
Popular Question 3.7 years ago, created a question with more than 1,000 views. For [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank

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