User: Chen
Chen • 730
- Reputation:
- 730
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- Website:
- http://chensun.pro/
- Last seen:
- 2 weeks, 4 days ago
- Joined:
- 6 years, 2 months 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
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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 9 weeks ago by
Chen • 730
• updated
9 weeks ago by
Friederike • 2.3k
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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 6 months ago by
Chen • 730
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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 6 months ago by
Chen • 730
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Comment:
C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 6 months ago by
Chen • 730
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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 6 months ago by
Chen • 730
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871
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9 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 6 months ago by
Chen • 730
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3
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8.0k
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3
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... is the database 0-based or 1 based? ...
written 6 months ago by
Chen • 730
1
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1.3k
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Comment:
C: BWA command guide
... The official BWA manual cite is down. ...
written 7 months ago by
Chen • 730
1
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1.3k
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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. ...
written 7 months ago by
Chen • 730
0
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3
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878
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3
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... 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 8 months ago by
Chen • 730
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