User: Chen
Chen • 770
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Computer Science Ph.D.
Fan of Istvan Albert
Research Area: Bioinformatics, Algorithms, Machine Learning
Posts by Chen
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... By contributing, I mean writing software or applications ...
written 3 months ago by
Chen • 770
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429
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8 follow
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... I got my Ph.D. in Computer Science with research directions of bioinformatics and computational biology.
I published several first-author papers in journal Bioinformatics and conferences like RECOMB.
I also have a Master degree in Genomics.
Now I am a full-time Software Engineer in Silicon Valley, ...
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... Here is 300x coverage NGS reads for human in FASTQ file format: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/ ...
written 3 months ago by
Chen • 770
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1
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... Previously people suggest me to put my tool into Galaxy, now people suggest me to put my tool into Bioconda.
After spending more than one day to put my recent tool into Bioconda, I am wondering does anyone know their differences? Which one is better to make your tool more accessible?
Thanks! ...
written 6 months ago by
Chen • 770
• updated
6 months ago by
Friederike ♦ 2.6k
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... I agree, and thank you for the information. I will double think before I ask next time. Please delete if possible. ...
written 10 months ago by
Chen • 770
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... Can SNP arrays such as Affymetrix genome-wide SNP array 6.0 handle clustered SNPs.
By clustered SNPs I mean SNPs that are very close to each other, for instance, SNPs that are closer than 10 bp? ...
written 10 months ago by
Chen • 770
0
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Comment:
C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 10 months ago by
Chen • 770
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1
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1.9k
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1
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... Hi swimmer, thank you very much for the suggestions. Do you think https://gencore.bio.nyu.edu/variant-calling-pipeline/ is a good command pipeline that I can follow? This is the kind of pipeline I am looking for, but I am not sure if they miss something important. ...
written 10 months ago by
Chen • 770
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1
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1.9k
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10 follow
1
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... With full respect, GATK is a good tool for SNP calling.
But the tutorial on GATK website is too complex, I get lost in the details.
Is there an easy to use a list of GATK commands for SNP calling? That I can copy and paste, with changing of just input file names, and maybe few parameters? ...
written 10 months ago by
Chen • 770
• updated
4 weeks ago by
francescomusacchia • 60
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5
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8.6k
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... is the database 0-based or 1 based? ...
written 11 months ago by
Chen • 770
Latest awards to Chen
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How to find the self aligned repeat region in human genome
Popular Question
3 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
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3 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
Popular Question
3 months ago,
created a question with more than 1,000 views.
For C++ tools are hard to install for biologist, why the community stick on it?
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4 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How to validate the SNP calling pipeline?
Good Question
4 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
Popular Question
5 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Appreciated
6 months ago,
created a post with more than 5 votes.
For Which Bioinformatics Tools Are Written In Python
Popular Question
7 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Popular Question
9 months ago,
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For C++ how to read VCF file in indexed bgzip format?
Great Question
10 months ago,
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For Which Bioinformatics Tools Are Written In Python
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voted more than 100 times.
Centurion
10 months ago,
created 100 posts.
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: How to validate the SNP calling pipeline?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How to find the self aligned repeat region in human genome
Popular Question
15 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Student
15 months ago,
asked a question with at least 3 up-votes.
For Which Bioinformatics Tools Are Written In Python
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16 months ago,
created a question with more than 1,000 views.
For How To Find The Most Frequent Allel Snp In Vcf File
Epic Question
21 months ago,
created a question with more than 10,000 views.
For Which Bioinformatics Tools Are Written In Python
Popular Question
21 months ago,
created a question with more than 1,000 views.
For How To Find The Most Frequent Allel Snp In Vcf File
Popular Question
21 months ago,
created a question with more than 1,000 views.
For How To Find The Most Frequent Allel Snp In Vcf File
Scholar
22 months ago,
created an answer that has been accepted.
For A: Can I get SNP information by individual from dbSNP
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