User: Ning-Yi Shao

gravatar for Ning-Yi Shao
Ning-Yi Shao390
Reputation:
390
Status:
Trusted
Location:
United States
Last seen:
6 years, 3 months ago
Joined:
10 years, 10 months ago
Email:
s*********@gmail.com

I am a postdoc fellow of Mount Sinai School of Medicine. Now I am focusing on the data analysis of ChIP-seq and RNA-seq. I got my PhD in July, 2011. I worked on the NGS datasets analysis in the group of Dr. Philipp Khaitovich in CAS-MPG Partner Institute for Computational Biology, Shanghai.

Posts by Ning-Yi Shao

<prev • 35 results • page 1 of 4 • next >
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Comment: C: How To Convert Chromosome Names Of Ensembl Annotation To The Ones Of Ucsc Refseq
... Thank you, Pierre. The information is interesting. It is the way to convert chromosome names of NCBI to of Ensembl way, is there the way to convert ucsc's to NCBI's? ...
written 7.7 years ago by Ning-Yi Shao390
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How To Convert Chromosome Names Of Ensembl Annotation To The Ones Of Ucsc Refseq Database?
... I am working on a database of many species. And I found the chromosome names of ensembl and refseq are terrible to convert between each other. I found there are tables named as ucscToEnsembl on UCSC, and they are great: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e "select * from uc ...
ensembl refseq chromosome written 7.7 years ago by Ning-Yi Shao390 • updated 12 months ago by max40
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Comment: C: Tools For De Novo Assembly Of Mirnas?
... For what I know, a friend of mine is developing a method to do such thing. He is in MDC, Berlin. They use reads to assemble contigs and use a naive Bayesian method to classify the result. But they haven't finish it yet. Genome Reference freE Prediction of miRNA : mirGREP It is the name of the method ...
written 9.0 years ago by Ning-Yi Shao390
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Answer: A: About The Prerequisite For Positive Selection
... I think the real stuff is the story beyond the theoretical signal. The signals are the direct clues of the selection story. But when the signal appears, we (I mean both computational biologist and wet lab biologist) should dig the story of the real world, the changing of exact environments and the c ...
written 9.0 years ago by Ning-Yi Shao390
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Comment: C: Inquiry Problem Of Bx-Python When I Extract Block From Different Strand In Maf F
... Thank you! Yes, it is done! ...
written 9.5 years ago by Ning-Yi Shao390
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Inquiry Problem Of Bx-Python When I Extract Block From Different Strand In Maf Files.
... Here I met a problem when I just followed this post to extract blocks from MAF files. Saying, the content of MAF named chr1_fake.maf is: ##maf version=1 a score=0.0 s SpeciesA.chr1 0 50 + 547496 acACTTGTGGCAGCATTGAAGGCTTCACTCTTCCCCAAGGGATATTATTA s SpeciesB.chr1 0 50 - 547496 acACTTG ...
python alignment multiple written 9.5 years ago by Ning-Yi Shao390 • updated 9.5 years ago by Brad Chapman9.5k
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Comment: C: How To Do Multiple Whole Genomes Alignments?
... Thank you very much! Now I am trying multiz and EPO pipeline. ...
written 9.6 years ago by Ning-Yi Shao390
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Comment: C: How To Do Multiple Whole Genomes Alignments?
... Now I am checking EPO pipeline, would you mind to give me more hint of the pipeline? For example, should I remove all repeat regions? Thank you very much! ...
written 9.6 years ago by Ning-Yi Shao390
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Comment: C: How To Do Multiple Whole Genomes Alignments?
... Thank you! But I need only three primates alignment. Is it possible to find a more detail description of the method to do the alignments? I hope to get exact whole genome alignments of Hg19, panTro3, and rheMac2. ...
written 9.6 years ago by Ning-Yi Shao390
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Comment: C: Execute Tophat Via Java
... Can you use exec("echo $PATH") to check $PATH of the java can find bowtie? ...
written 9.6 years ago by Ning-Yi Shao390

Latest awards to Ning-Yi Shao

Popular Question 6.7 years ago, created a question with more than 1,000 views. For How To Do Multiple Whole Genomes Alignments?
Appreciated 7.0 years ago, created a post with more than 5 votes. For A: Phastcons Files
Popular Question 7.0 years ago, created a question with more than 1,000 views. For How To Do Multiple Whole Genomes Alignments?
Supporter 7.0 years ago, voted at least 25 times.
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: Cannot Install Latest Version Of Deseq
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: Phastcons Files
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?
Student 7.0 years ago, asked a question with at least 3 up-votes. For How To Do Multiple Whole Genomes Alignments?
Autobiographer 7.0 years ago, has more than 80 characters in the information field of the user's profile.

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