User: Peter Chung
Peter Chung • 70
- Reputation:
- 70
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- Trusted
- Location:
- Hong Kong
- Last seen:
- 3 months, 1 week ago
- Joined:
- 1 year, 11 months ago
- Email:
- q*************@gmail.com
Posts by Peter Chung
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... 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 ...
written 3 months ago by
Peter Chung • 70
• updated
3 months ago by
Ram ♦ 17k
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... 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 ...
written 4 months ago by
Peter Chung • 70
• updated
4 months ago by
dariober ♦ 9.3k
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... 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 ...
written 13 months ago by
Peter Chung • 70
• updated
11 months ago by
Biostar ♦♦ 20
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... 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 17 months ago by
Peter Chung • 70
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6 follow
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... 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 ...
written 17 months ago by
Peter Chung • 70
• updated
15 months ago by
ShirleyDai • 30
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8 follow
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... 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 ...
written 18 months ago by
Peter Chung • 70
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... 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 ...
written 23 months ago by
Peter Chung • 70
• updated
3 months ago by
Kevin Blighe ♦ 26k
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... @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 23 months ago by
Peter Chung • 70
1
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... 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
...
written 23 months ago by
Peter Chung • 70
• updated
21 months ago by
Nico Gerstner • 0
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... 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 ...
written 23 months ago by
Peter Chung • 70
• updated
23 months ago by
nwon • 20
Latest awards to Peter Chung
Appreciated
3 months ago,
created a post with more than 5 votes.
For question about the impute2 output format
Popular Question
11 months ago,
created a question with more than 1,000 views.
For TCGA UUID change back to TCGAbarcode
Popular Question
11 months ago,
created a question with more than 1,000 views.
For looking for TCGA gene expression Normal Samples
Student
11 months ago,
asked a question with at least 3 up-votes.
For question about the impute2 output format
Supporter
18 months ago,
voted at least 25 times.
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