User: Shicheng Guo

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Shicheng Guo6.5k
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Posts by Shicheng Guo

<prev • 454 results • page 1 of 46 • next >
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How to access AMED-CREST methylation dataset
... I want to download and re-analysis AMED-CREST methylation dataset. Who knows how to access it? http://epigenomesportal.ca/ihec/download.html?b=2017-10&as=1&i=7&ctc=23&session=8652 Thanks. ...
amed-crest written 17 days ago by Shicheng Guo6.5k
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Multiple Haplotype Phasing Solutions in Plink
... Plink really does a great job when it calculate LD and even for multiple haplotypes/phasings, LDs are provided. However, the posterior probability were lost, right? How to choose the best one when it happened like this situation? > --ld rs998731 rs77356712: Multiple haplotype phasing solut ...
plink ld written 24 days ago by Shicheng Guo6.5k • updated 24 days ago by chrchang5233.9k
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Comment: C: Awk in Bioinformatics
... Yes. I just record it for myself. and I am happy if it helps others. if not, I am sure it is no harm to others, right? ...
written 24 days ago by Shicheng Guo6.5k
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Comment: C: Fast way to extract part of genotypes data from 1000 Genome VCF files
... Great try. Thanks fin swimmer! ...
written 24 days ago by Shicheng Guo6.5k
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Forum: Awk in Bioinformatics
... Here to show the examples to use awk with powerful recombination: I will update more examples. 1. Merge column 4 and 5 and ouput to the file named as column 1 and 3. ``` awk '{print $4"\n"$5 > "./snpset/$1.$3.txt}' GRCH37.SNP150.bed ``` 2. Split and print content to it (as filename) ``` awk ...
perl forum pbs shell awk written 25 days ago by Shicheng Guo6.5k
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Comment: C: Fast way to extract part of genotypes data from 1000 Genome VCF files
... Great suggestion. Thanks.Chris!! It will try plink 2.0 more ...
written 25 days ago by Shicheng Guo6.5k
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Comment: C: Fast way to extract part of genotypes data from 1000 Genome VCF files
... it will be perfect if tabix could accept rs number as the input. ...
written 26 days ago by Shicheng Guo6.5k
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Answer: A: Fast way to extract part of genotypes data from 1000 Genome VCF files
... With the help of tabix, just few minutes rather than days to complete the LD use strict; use Cwd; my $dir=getcwd; chdir $dir; my $genome="/gpfs/home/guosa/hpc/db/hg19/1000Genome"; mkdir "Shuffle" if ! -e "Shuffle"; my $file="/gpfs/home/guosa/nc/GWAS-378.DMER.bed.sort.bed ...
written 26 days ago by Shicheng Guo6.5k
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Fast way to extract part of genotypes data from 1000 Genome VCF files
... Hi All, I need to do some permutation test to random sampling millions of SNPs set genotyping data from 1000 genome phase III dataset. each SNP-set only contains ~300 SNPs, however, I found the extract process is quite slow. for example, for the ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130 ...
fast vcf 1000genome written 27 days ago by Shicheng Guo6.5k • updated 26 days ago by chrchang5233.9k
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Answer: A: Check if REF allele is minor allele in any variant
... In terms of phase III data-set from [1000 Genome project, only 2149549/84802133=2.5%][1] have >50% or higher Alternative allele frequency. It make sense since human genome is derived from several individual human genome and therefore, the reference genome should have high probability to be major ...
written 29 days ago by Shicheng Guo6.5k

Latest awards to Shicheng Guo

Student 17 days ago, asked a question with at least 3 up-votes. For Public data access: Single-cell RNA-seq and Buck RNA-seq data
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: error in running R
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: error in running R
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: error in running R
Student 5 weeks ago, asked a question with at least 3 up-votes. For Public data access: Single-cell RNA-seq and Buck RNA-seq data
Scholar 6 weeks ago, created an answer that has been accepted. For A: significant differential expressed gene validation
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bad Exprience on bigwig Format Visualization in UCSC
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Bad Exprience on bigwig Format Visualization in UCSC
Student 8 weeks ago, asked a question with at least 3 up-votes. For Public data access: Single-cell RNA-seq and Buck RNA-seq data
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Bad Exprience on bigwig Format Visualization in UCSC
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: error in running R
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 3 months ago, created a question with more than 1,000 views. For Bad Exprience on bigwig Format Visualization in UCSC
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: error in running R
Great Question 3 months ago, created a question with more than 5,000 views. For fastq-dump split-spot and skip-technical
Popular Question 3 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 3 months ago, created a question with more than 1,000 views. For Bad Exprience on bigwig Format Visualization in UCSC
Popular Question 4 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 4 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Student 5 months ago, asked a question with at least 3 up-votes. For Public data access: Single-cell RNA-seq and Buck RNA-seq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: error in running R
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Fastqc to BS-seq dataset (Methylation-seq quality control)
Prophet 5 months ago, created a post with more than 20 followers. For Good Habit for Bioinformatics Analyst or Scientist
Popular Question 5 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10
Popular Question 5 months ago, created a question with more than 1,000 views. For Vector NTI in Window 10

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