User: Peter Chung

gravatar for Peter Chung
Peter Chung70
Reputation:
70
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Trusted
Location:
Hong Kong
Last seen:
1 week, 5 days ago
Joined:
1 year, 8 months ago
Email:
q*************@gmail.com

Posts by Peter Chung

<prev • 10 results • page 1 of 1 • next >
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use gatk phased vcf as input file of HapCut2
... I am new in sequencing analysis and would like to do haplotype blocks from the result of WGS. But I have some questions on the HAPCUT2. I generated a vcf from gatk and then I phased it using gatk ReadBackedPhasing into phased vcf. Commands below are from HAPCUT2: ./build/extractHAIRS [options ...
hapcut2 gatk vcf phasing written 15 days ago by Peter Chung70 • updated 5 days ago by Ram15k
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bwa mem without -M option how to continue using picard
... I do the alignment without -M option and now I have all the bam file and would like to do the downstream steps using picard and GATK, what can I do to restore the -M option except realign all the fastq because I have more than hundreds fastq files. Thank you ...
assembly sequence sequencing written 6 weeks ago by Peter Chung70 • updated 5 weeks ago by dariober9.1k
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is it .impute2 format equal to .gen format
... I would like to apply qctool software from .impute2 format to .bgen format. However, qctool -g HELLO.impute2 -og HELLO.bgen Error comes out: !! Error (genfile::BadArgumentError): In argument(s) filetype_hint="guess", inferred type = "" to function genfile::SNPDataSource::create(): Unrecognised f ...
impute2 imputation qctool written 10 months ago by Peter Chung70 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Subsetting individuals from IMPUTE2 ref files: .hap and .legend
... I have that question too, https://www.biostars.org/p/239067/ do you know how to do it now? I would like to extract CHS CHB population out from .sample, .legend and .hap file of impute2 reference data phase3. ...
written 14 months ago by Peter Chung70
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imputation only choose one population as reference panel
... I have a gwas data to do the imputation by shapeit2 and impute2. I would like to use only east asians population in 1,000 Genomes haplotypes -- Phase 3 integrated variant set release in NCBI build 37 (hg19) coordinates from impute2 reference data: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3 ...
shapeit impute2 population gwas written 14 months ago by Peter Chung70 • updated 12 months ago by ShirleyDai20
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question about the impute2 output format
... I have a large snp data in plink format. I used shapeit2 to do the phasing steps and output file is gwas.phased.haps gwas.phased.sample which is normal. .haps file: 22 rs35416799 16869887 A G 22 rs115144709 17000277 A G 22 rs5746642 17055818 A G and then I used the gwas.phased.hap ...
gwas imputation snp written 15 months ago by Peter Chung70
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TCGA UUID change back to TCGAbarcode
... I downloaded the RNA Seq data TCGA Legacy Archive, all the rsem.gene.normalized_results is UUID, how can I know the TCGA barcode back because I can't identify the normal samples and tumor samples. But the isoform.quantitifcation has the TCGA barcode name, so i was confused, can anyone explain it t ...
tcga rna-seq written 20 months ago by Peter Chung70 • updated 9 days ago by Kevin Blighe19k
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Comment: C: looking for TCGA gene expression Normal Samples
... @nwon I tried to put 11 or 11a in the case id but it had shown not found anything and can you show me which field should i add in the biospecimen filter ? ...
written 20 months ago by Peter Chung70
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Questions: rsem.genes.normalized. data in GDC Legacy Archive file name to identify normal and tumor samples
... I am new in TCGA GDC Legacy Archive. I would like to ask some questions about it. I downloaded a list of gene expression files below unc.edu.a2b8f7d7-3e9b-4e7f-9198-fb1d75a2eb0a.2563597.rsem.genes.normalized_results unc.edu.f5487583-cdac-42ba-8f7f-b1704ea21cad.2331596.rsem.genes.normalized_results ...
tcga rna-seq written 20 months ago by Peter Chung70 • updated 18 months ago by Nico Gerstner0
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looking for TCGA gene expression Normal Samples
... I am looking for the matched cancer samples and normal samples in TCGA. I used to download these data before but now I seem like can't find the normal samples from the TCGA legacy archive. I looked up the TCGA barcode and the samples all are cancer sample label 01 but didn't have 11 for the normal ...
genome sequence written 20 months ago by Peter Chung70 • updated 20 months ago by nwon20

Latest awards to Peter Chung

Appreciated 22 days ago, created a post with more than 5 votes. For question about the impute2 output format
Popular Question 8 months ago, created a question with more than 1,000 views. For TCGA UUID change back to TCGAbarcode
Popular Question 8 months ago, created a question with more than 1,000 views. For looking for TCGA gene expression Normal Samples
Student 8 months ago, asked a question with at least 3 up-votes. For question about the impute2 output format
Supporter 15 months ago, voted at least 25 times.

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