User: Yongjie Zhang
Yongjie Zhang • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- UC Berkeley, USA/ Shanxi Univ, China
- Website:
- http://scholar.google....
- Last seen:
- 1 month, 4 weeks ago
- Joined:
- 6 years, 3 months ago
- Email:
- y***************@gmail.com
about me
Posts by Yongjie Zhang
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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 4 months ago by
Yongjie Zhang • 80
• updated
4 months ago by
lieven.sterck ♦ 7.9k
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... Dear Pierre,
Could you please give more details? ...
written 2.5 years ago by
Yongjie Zhang • 80
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2
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1.6k
views
5 follow
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... 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 ...
written 2.5 years ago by
Yongjie Zhang • 80
• updated
2.5 years ago by
natallah • 10
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... 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 ...
written 2.5 years ago by
Yongjie Zhang • 80
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... 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? ...
written 3.0 years ago by
Yongjie Zhang • 80
• updated
23 months ago by
Biostar ♦♦ 20
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... 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 3.9 years ago by
Yongjie Zhang • 80
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... 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 ...
written 3.9 years ago by
Yongjie Zhang • 80
0
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1.2k
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... 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
...
written 4.0 years ago by
Yongjie Zhang • 80
• updated
23 months ago by
Biostar ♦♦ 20
0
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1.6k
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... 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 4.0 years ago by
Yongjie Zhang • 80
0
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1
answer
1.6k
views
1
answer
... 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 ...
written 4.0 years ago by
Yongjie Zhang • 80
• updated
4.0 years ago by
dariober ♦ 11k
Latest awards to Yongjie Zhang
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2.5 years ago,
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created a question with more than 1,000 views.
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created a question with more than 1,000 views.
For How to blast against published transcriptome data
Great Question
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For Joining Paired-End Illumina Raw Reads
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For Building a tree for binary data
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3.0 years ago,
created a question with more than 1,000 views.
For Programs for drawing a circular mitochondrial map, Circos or others?
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For How to blast against published transcriptome data
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3.3 years ago,
created a question with more than 1,000 views.
For Building a tree for binary data
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3.8 years ago,
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