User: Peter Chung

gravatar for Peter Chung
Peter Chung120
Reputation:
120
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Trusted
Location:
Hong Kong
Last seen:
2 months, 3 weeks ago
Joined:
4 years ago
Email:
q*************@gmail.com

Posts by Peter Chung

<prev • 30 results • page 1 of 3 • next >
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Answer: A: snakemake output directory
... I can successfully output the result to the result directory. rule run_fastqc: input: "data/ERR127302_1_subset.fastq.gz" output: "result/{sample}_fastqc.html", "result/{sample}_fastqc.zip" params: dir="result" shell: ...
written 3 months ago by Peter Chung120
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Comment: C: snakemake output directory
... no, I didn't. what should I input in rule all rule all: input: expand("result/{sample}_fastqc.html",sample=SAMPLES), expand("result/{sample}_fastqc.zip",sample=SAMPLES) it stills output at the data directory ...
written 3 months ago by Peter Chung120
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Comment: C: snakemake output directory
... I want the fastqc output file, the html file and the zip file output to result directory but it output nothing. I tried to change the output in the Snakefile like below: output: expand("result/{sample}_fastqc.html",sample=SAMPLES), expand("result/{sample}_fastqc.zip",sample=SAMPLES) but i ...
written 3 months ago by Peter Chung120
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snakemake output directory
... I am new to snakemake. I have a simple quesiton and I can not do the fastqc output into a directory rule run_fastqc: input: "data/ERR127302_1_subset.fastq.gz" output: directory("result/") shell: "fastqc {input} -o {output} " I try the command: snak ...
ngs snakemake written 3 months ago by Peter Chung120
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Comment: C: gatk collectallelic counts error
... yes. tried. no variables in the script. same error came out. ...
written 3 months ago by Peter Chung120
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Comment: C: gatk collectallelic counts error
... I already subset the bam file from 10X to 1X but the error is still there. I used the gatk4.1.7 in conda environment. ...
written 3 months ago by Peter Chung120
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Comment: C: gatk collectallelic counts error
... yes I tried to subset the bam file and interval file as well. but also have similar error [May 22, 2020 12:15:40 PM HKT] org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCounts done. Elapsed time: 21.76 minutes. Runtime.totalMemory()=15772155904 Exception in thread "main" java.lang.OutO ...
written 4 months ago by Peter Chung120
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Comment: C: gatk collectallelic counts error
... mkdir tmp TMPFILE=$(`pwd`)/tmp a temporary directory ...
written 4 months ago by Peter Chung120
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gatk collectallelic counts error
... I am running the gatk collect allelic counts function, but there is an error that I don't know how to fix. Interval list is downloaded from gatk resource bundle: https://storage.cloud.google.com/genomics-public-data/resources/broad/hg38/v0/wgs_calling_regions.hg38.interval_list and then I use gatk ...
gatk java written 4 months ago by Peter Chung120
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Comment: C: Haplotype resolving (phasing) from BAM file
... almost 4 years, I think he is still working on it, lets be patient ...
written 4 months ago by Peter Chung120

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Popular Question 17 months ago, created a question with more than 1,000 views. For looking for TCGA gene expression Normal Samples
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For question about the impute2 output format
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Appreciated 2.4 years ago, created a post with more than 5 votes. For question about the impute2 output format
Popular Question 3.0 years ago, created a question with more than 1,000 views. For TCGA UUID change back to TCGAbarcode
Popular Question 3.0 years ago, created a question with more than 1,000 views. For looking for TCGA gene expression Normal Samples
Student 3.0 years ago, asked a question with at least 3 up-votes. For question about the impute2 output format
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