User: Chen
Chen • 990
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- 11 months, 1 week ago
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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 20 months ago by
Chen • 990
8
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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 20 months ago by
Chen • 990
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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 23 months ago by
Chen • 990
• updated
23 months ago by
Friederike ♦ 5.7k
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488
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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 2.2 years ago by
Chen • 990
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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 2.2 years ago by
Chen • 990
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Comment:
C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 2.3 years ago by
Chen • 990
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2
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6.3k
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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 2.3 years ago by
Chen • 990
11
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2
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6.3k
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15 follow
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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 2.3 years ago by
Chen • 990
• updated
15 months ago by
johannes.koester • 10
0
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5
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... is the database 0-based or 1 based? ...
written 2.3 years ago by
Chen • 990
Latest awards to Chen
Great Question
14 months ago,
created a question with more than 5,000 views.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
Student
17 months ago,
asked a question with at least 3 up-votes.
For Which Bioinformatics Tools Are Written In Python
Student
17 months ago,
asked a question with at least 3 up-votes.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: How to validate the SNP calling pipeline?
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Question about genotype phased PQ and PS in VCF file format 4.1
Popular Question
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created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
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20 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Good Question
20 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
Popular Question
20 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?
Popular Question
20 months ago,
created a question with more than 1,000 views.
For How to find the self aligned repeat region in human genome
Good Question
21 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: How to validate the SNP calling pipeline?
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21 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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22 months ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Appreciated
22 months ago,
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For Which Bioinformatics Tools Are Written In Python
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24 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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2.1 years ago,
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For C++ how to read VCF file in indexed bgzip format?
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2.2 years 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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2.2 years ago,
created a question with more than 5,000 views.
For Which Bioinformatics Tools Are Written In Python
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2.3 years ago,
voted more than 100 times.
Centurion
2.3 years ago,
created 100 posts.
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For C++ how to read VCF file in indexed bgzip format?
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: How to validate the SNP calling pipeline?
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For How to find the self aligned repeat region in human genome
Popular Question
2.7 years 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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