User: haiying.kong
haiying.kong • 160
- Reputation:
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- Germany
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Posts by haiying.kong
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... When I run the sample command line with sample data for OncodriveFML, I got the error message:
(OncodriveFML) kong@cloud-hpc-06-kong:~/Haiying/Projects/PrimaryMelanoma/temp> oncodrivefml -i paad.txt.gz -e cds.regions.gz --type coding --sequencing wes -c oncodrivefml.conf
ERROR:root:Impossible to ...
written 26 days ago by
haiying.kong • 160
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112
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Answer:
A: Main title on RCircos plot
... functions locator and text can do the job. ...
written 4 weeks ago by
haiying.kong • 160
0
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112
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... I am plotting Circos plots with RCircos CRAN package.
I would like to have a main title on the top of each circos plot.
How can I do this? ...
written 4 weeks ago by
haiying.kong • 160
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119
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... I have 2 patients, each of which has normal, primary, and metastatic samples whole exome sequenced.
If I compare somatic mutations in primary and metastatic samples
Patient 1:
N_somatic_mutations_primary N_somatic_mutations_metastatic N_intersection
532 ...
written 7 weeks ago by
haiying.kong • 160
• updated
7 weeks ago by
Dan Gaston ♦ 6.8k
1
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... Dear Manuel,
The website is saying
"What genome build is the gnomAD data based on?
All data are based on GRCh37/hg19"
http://gnomad.broadinstitute.org/faq ...
written 8 weeks ago by
haiying.kong • 160
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... Could you please give me complete list of database you use as reference for germline mutations for hg19/hg37?
It would be wonderful if you could give me links to download as well :) ...
written 8 weeks ago by
haiying.kong • 160
1
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179
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... primary melanoma whole exome sequence. ...
written 8 weeks ago by
haiying.kong • 160
0
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1
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179
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1
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... Could you please tell me which database you use as germline mutation list? ...
written 8 weeks ago by
haiying.kong • 160
7
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1
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179
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1
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... I have WES for 6 tumors which do not have matching normals. I identified all mutations, both germline and somatic with GATK. Then excluded all mutations that are considered as germline by ExAC, and germline mutations that are identified from our about 90 normal samples.
The number of somatic mutatio ...
written 8 weeks ago by
haiying.kong • 160
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139
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... I am trying to filter variants by following the recommended steps on the manual.
Our data is WES for paired samples of normal and tumor. Average depth is 60.
If I run the following commands they all give empty output files without any errors.
I checked all input files, and they are correct. Tweaked ...
written 8 weeks ago by
haiying.kong • 160
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