User: Chen
Chen • 690
- Reputation:
- 690
- Status:
- Trusted
- Location:
- 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 >
2
votes
1
answer
156
views
1
answer
... 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 7 days ago by
Chen • 690
• updated
7 days ago by
Friederike • 2.0k
0
votes
0
answers
124
views
0
answers
... 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
Chen • 690
0
votes
0
answers
124
views
0
answers
... 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 4 months ago by
Chen • 690
0
votes
0
answers
150
views
0
answers
Comment:
C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 4 months ago by
Chen • 690
0
votes
0
answers
441
views
0
answers
... 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
Chen • 690
6
votes
0
answers
441
views
9 follow
0
answers
... 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 4 months ago by
Chen • 690
0
votes
3
answers
7.7k
views
3
answers
... is the database 0-based or 1 based? ...
written 4 months ago by
Chen • 690
1
vote
0
answers
792
views
0
answers
Comment:
C: BWA command guide
... The official BWA manual cite is down. ...
written 5 months ago by
Chen • 690
1
vote
0
answers
792
views
0
answers
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. ...
written 5 months ago by
Chen • 690
0
votes
3
answers
728
views
3
answers
... 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
Chen • 690
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
Appreciated
2.0 years ago,
created a post with more than 5 votes.
For Which Journals Should I Follow If I Write Software And Algorithms In Computational Biology?
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
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For Which Bioinformatics Tools Are Written In Python
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 905 users visited in the last hour