User: Yongjie Zhang

gravatar for Yongjie Zhang
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Location:
UC Berkeley, USA/ Shanxi Univ, China
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http://scholar.google....
Last seen:
7 hours ago
Joined:
5 years, 11 months ago
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Posts by Yongjie Zhang

<prev • 53 results • page 1 of 6 • next >
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Answer: A: MaSuRCA installation error
... Boost is not found. You have two options: 1. implement the command `BOOST_ROOT=install ./install.sh` Download and decompress boost (https://sourceforge.net/projects/boost/files/boost/), and then 2. implement the command like `BOOST_ROOT=/share/home/zhangyj/biosoft/boost_1_72_0 ./install.s ...
written 10 days ago by Yongjie Zhang80 • updated 7 days ago by lieven.sterck6.9k
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Comment: C: How to orient and order a bundle of sequences based on a reference sequence
... Dear Pierre, Could you please give more details? ...
written 2.1 years ago by Yongjie Zhang80
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(Closed) how to sort fasta format DNA sequences based on a given sequence name list
... Hello, I have a fasta file with many DNA sequences. I want to sort these sequence based on a designated order in a sequence name list file. How to acheive this? Thanks. Yongjie ...
sort fasta sequences written 2.1 years ago by Yongjie Zhang80 • updated 2.1 years ago by natallah10
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How to orient and order a bundle of sequences based on a reference sequence
... Hello, I have dozens of contig sequences representing mitochondral fragments of a species, and want to orient and order these sequences by refering to a reference mitochondrial genome sequence. I used to do it by hand, but do you know an easy way to do this? Any programs or scripts? Thanks, Yongj ...
orient and order sequences written 2.1 years ago by Yongjie Zhang80
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Draw AT content plot across a DNA sequence
... I want to draw a base composition plot in a DNA sequence, but currently programs (e.g., http://www.ebi.ac.uk/Tools/seqstats/emboss_cpgplot/) only plot GC contents. Did you know how to plot AT contents across a DNA sequence? ...
plot at contents written 2.7 years ago by Yongjie Zhang80 • updated 18 months ago by Biostar ♦♦ 20
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Comment: C: Displaying a virtual electrophoresis map
... Thanks for your answer, but my question seems not be solved. I hope to input a DNA sequence (as templates) and some primer pairs. Then,the tool can generate a virtual electrophoretic gel image, where each lane correpsonds to the amplification result of a primer pair. ...
written 3.6 years ago by Yongjie Zhang80
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(Closed) What's the best way of generating high yields of mitochondrial DNA
... Hello, I want to extract mitochondrial DNA from a fungus, but there are two ways to cultivate the fungus, one is to cultivate it on an agar medium (covering a piece of cellophane paper to stop hyphae to grow into the medium) in a petri dish, and the other is to cultivate it in a liquid medium in an ...
mitochondrial dna written 3.6 years ago by Yongjie Zhang80
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Displaying a virtual electrophoresis map
... Hello, I want to display a virtual electrophoresis map based on a DNA template (i.e. a long DNA sequence) and some primer pairs. I do not want to do PCR experiment and run a real gel. Do you know if there is a tool to help me? Thanks for any comments. Yongjie ...
electrophoresis map pcr written 3.6 years ago by Yongjie Zhang80 • updated 19 months ago by Biostar ♦♦ 20
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Comment: C: On calculating RPKM values for RNA-seq data
... Thank you, dariober. I noticed that some literature considered a gene was expressed if RPKM > 0.2. Do you think if such a threshold value (0.2) widely recognized in the community? In my case, RPKM for some mitochondrial genes will be lower than 0.2 if I use the whole reads instead of only mitocho ...
written 3.6 years ago by Yongjie Zhang80
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On calculating RPKM values for RNA-seq data
... Hello, I performed RNA-seq for a sample and want to calculate RPKM values. But I have two questions for your help. 1) Since paired-end Illumina sequencing was performed, can I use either single reads or fragments (i.e. paired reads) to calculate RPKM? 2) Let's suppose the total numbers of clean r ...
rpkm written 3.6 years ago by Yongjie Zhang80 • updated 3.6 years ago by dariober11k

Latest awards to Yongjie Zhang

Popular Question 13 months ago, created a question with more than 1,000 views. For How to perform neutrality test and how to understand its output
Popular Question 13 months ago, created a question with more than 1,000 views. For How to test if two phylogenies are statistically consistent
Popular Question 13 months ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 13 months ago, created a question with more than 1,000 views. For How to blast against published transcriptome data
Popular Question 20 months ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 20 months ago, created a question with more than 1,000 views. For Programs for drawing a circular mitochondrial map, Circos or others?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to blast against published transcriptome data
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Programs for drawing a circular mitochondrial map, Circos or others?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to blast against published transcriptome data
Great Question 2.7 years ago, created a question with more than 5,000 views. For Joining Paired-End Illumina Raw Reads
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Programs for drawing a circular mitochondrial map, Circos or others?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to blast against published transcriptome data
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Building a tree for binary data
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Joining Paired-End Illumina Raw Reads
Popular Question 3.8 years ago, created a question with more than 1,000 views. For About Outgroups In Phylogenetic Analysis
Popular Question 4.3 years ago, created a question with more than 1,000 views. For About Outgroups In Phylogenetic Analysis
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Joining Paired-End Illumina Raw Reads

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