User: Peter Chung
Peter Chung • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- Hong Kong
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 4 years ago
- Email:
- q*************@gmail.com
Posts by Peter Chung
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1
vote
2
answers
180
views
2
answers
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 Chung • 120
0
votes
2
answers
180
views
2
answers
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 Chung • 120
0
votes
2
answers
180
views
2
answers
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 Chung • 120
3
votes
2
answers
180
views
2
answers
... 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 ...
written 3 months ago by
Peter Chung • 120
0
votes
0
answers
146
views
0
answers
Comment:
C: gatk collectallelic counts error
... yes. tried. no variables in the script. same error came out. ...
written 3 months ago by
Peter Chung • 120
0
votes
0
answers
146
views
0
answers
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 Chung • 120
0
votes
0
answers
146
views
0
answers
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 Chung • 120
0
votes
0
answers
146
views
0
answers
Comment:
C: gatk collectallelic counts error
... mkdir tmp
TMPFILE=$(`pwd`)/tmp
a temporary directory ...
written 4 months ago by
Peter Chung • 120
1
vote
0
answers
146
views
0
answers
... 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 ...
written 4 months ago by
Peter Chung • 120
1
vote
0
answers
2.1k
views
0
answers
... almost 4 years, I think he is still working on it, lets be patient ...
written 4 months ago by
Peter Chung • 120
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