User: Chen
Chen • 650
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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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... I agree, and thank you for the information. I will double think before I ask next time. Please delete if possible. ...
written 4 days ago by
Chen • 650
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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 12 days ago by
Chen • 650
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Comment:
C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 17 days ago by
Chen • 650
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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 18 days ago by
Chen • 650
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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 18 days ago by
Chen • 650
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... is the database 0-based or 1 based? ...
written 25 days ago by
Chen • 650
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Comment:
C: BWA command guide
... The official BWA manual cite is down. ...
written 7 weeks ago by
Chen • 650
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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 weeks ago by
Chen • 650
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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 10 weeks ago by
Chen • 650
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... **The recommended benchmark dataset is from NIST(National Institute of Standards and Technology) GIAB. They update frequently with new data and sequencing tech**
Paper: https://www.nature.com/articles/nbt.2835
Data download: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GR ...
written 10 weeks ago by
Chen • 650
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