User: Chen

gravatar for Chen
Chen690
Reputation:
690
Status:
Trusted
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Website:
http://chensun.pro/
Last seen:
1 day, 22 hours ago
Joined:
6 years ago
Email:
b********@gmail.com

Computer Science PhD @ Penn State

Applied Researcher @ Linkedin / Microsoft

Fan of Istvan Albert 

Research Area: Bioinformatics, Algorithms, Machine Learning

Posts by Chen

<prev • 97 results • page 1 of 10 • next >
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What is the difference between Bioconda and Galaxy?
... 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! ...
bioconda galaxy bioinformatics tools written 7 days ago by Chen690 • updated 7 days ago by Friederike2.0k
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Comment: C: Can SNP array handle clustered SNPs
... I agree, and thank you for the information. I will double think before I ask next time. Please delete if possible. ...
written 4 months ago by Chen690
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Can SNP array handle clustered SNPs
... 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? ...
snp calling snp array snp written 4 months ago by Chen690
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Comment: C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 4 months ago by Chen690
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Comment: C: Is there a easy to use GATK pipeline for SNP calling?
... 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 4 months ago by Chen690
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9 follow
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Is there a easy to use GATK pipeline for SNP calling?
... 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? ...
gatk written 4 months ago by Chen690
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Comment: C: Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
... is the database 0-based or 1 based? ...
written 4 months ago by Chen690
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Comment: C: BWA command guide
... The official BWA manual cite is down. ...
written 5 months ago by Chen690
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Page: BWA command guide
... **SYNOPSIS** bwa index ref.fa bwa mem ref.fa reads.fq > aln-se.sam bwa mem ref.fa read1.fq read2.fq > aln-pe.sam bwa aln ref.fa short_read.fq > aln_sa.sai bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe. ...
page bwa written 5 months ago by Chen690
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Comment: C: How to validate the SNP calling pipeline?
... VarMatch provides 2x2x3 = 12 different strategy combinations to validate, and they are all very simple and straightforward to understand. In certain conditions, different strategies can lead to different conclusions about whether your pipeline is better than others. I would recommend the default str ...
written 6 months ago by Chen690

Latest awards to Chen

Popular Question 5 weeks ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
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?
Great Question 4 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Voter 4 months ago, voted more than 100 times.
Centurion 4 months ago, created 100 posts.
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?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to validate the SNP calling pipeline?
Popular Question 9 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, created a question with more than 1,000 views. For How to find the self aligned repeat region in human genome
Student 9 months ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 10 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 15 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 15 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 15 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Scholar 15 months ago, created an answer that has been accepted. For A: Can I get SNP information by individual from dbSNP
Epic Question 2.0 years ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Good Question 2.0 years ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Epic Question 2.1 years ago, created a question with more than 10,000 views. For How To Sort Sam File
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Delly: how does delly decide whether a SV is imprecise or precise
Great Question 2.3 years ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 2.4 years ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python

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