User: haiying.kong

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haiying.kong170
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170
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Location:
Germany
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2 months, 3 weeks ago
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2 years ago
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Posts by haiying.kong

<prev • 99 results • page 1 of 10 • next >
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OncodriveFML --- ERROR:root:Impossible to download.
... 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 ...
oncodrivefml written 12 weeks ago by haiying.kong170
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Answer: A: Main title on RCircos plot
... functions locator and text can do the job. ...
written 3 months ago by haiying.kong170
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Main title on RCircos plot
... 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? ...
rcircos written 3 months ago by haiying.kong170
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Tumor Progress Study
... 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 ...
wes written 3 months ago by haiying.kong170 • updated 3 months ago by Dan Gaston6.8k
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... 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 3 months ago by haiying.kong170
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... 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 4 months ago by haiying.kong170
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... primary melanoma whole exome sequence. ...
written 4 months ago by haiying.kong170
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... Could you please tell me which database you use as germline mutation list? ...
written 4 months ago by haiying.kong170
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Somatic Mutation Identification for Tumor without Normal
... 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 ...
somatic mutation written 4 months ago by haiying.kong170
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Comment: C: Meerkat for identification of somatic structural variations for paired samples
... 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 4 months ago by haiying.kong170

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