User: yussab

gravatar for yussab
yussab10
Reputation:
10
Status:
New User
Location:
Italy
Last seen:
4 days, 16 hours ago
Joined:
7 months, 2 weeks ago
Email:
a***********@hotmail.it

I come from a multicultural background, my life experiences have given me a broad point of view and mindset that I have applied to everything I do.
During my studies I achieved a 360 view of biopharma industry. Starting from basic research to the elaboration of big data on RNA-seq and the economic skills to exploit invention through patents and marketing strategies.

Posts by yussab

<prev • 19 results • page 1 of 2 • next >
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Comment: C: VEP for cancer annotation using COSMIC
... Dear Emily, I filtered my vcf file using this command: > filter_vep -i Mutect2_filtered_VEP.ann.vcf.gz -o out_filtered_SOMATIC.vcf --filter "SOMATIC" I obtain the result in the table, however I'm still confused on how to interpret these vcf file. **filtering_status=These calls have been filter ...
written 14 days ago by yussab10
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Comment: C: VEP for cancer annotation using COSMIC
... Thank you Emily, I'll try and let you know how it worked! :) ...
written 16 days ago by yussab10
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VCF files unannotated files from The Cancer Genome Atlas
... Dear community, I would like to download vcf data from The Cancer Genome Atlas to perform annotation and testing OncoKB. I do not understand if I should apply to control data access or if the vcf data are availables to researcher?? If I try to download data from this link: https://portal.gdc.canc ...
vcf tcga written 16 days ago by yussab10
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VEP for cancer annotation using COSMIC
... Dear all, I'm struggling in finding how to obtain information about COSMIC database after I annotate a vcf using VEP. The command that I used is: vep -i Mutect2_unfiltered_10643_vs_2434.vcf.gz -o Mutect2_unfiltered_10643_vs_2434_VEP.ann.vcf --assembly GRCh38 --specie ...
cosmic vep cancer written 16 days ago by yussab10 • updated 16 days ago by Emily_Ensembl21k
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GATK GenomicDBImport missing argument --intervals for Illumina HiSeq Exome??
... Hi everyone, I'm using the GATK germline short variant discovery (SNPs + Indels) pipeline. https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- After using HaplotypeCaller to call the GVCF, I'm not consolidating the variants using GenomicsDB ...
exome gatk genomicdbimport illumina written 3 months ago by yussab10
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Comment: C: Reproduce Genome in a Bottle analysis from NA12878 fastq?
... Hi a.alnawfal.1992, thank you for your kind answer... So it's not necessary to process the Variant Filtration/Refine Genotypes/Variant Annotation steps??? In this way you use raw vcf snps + indels?? ...
written 3 months ago by yussab10
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Answer: A: There is a convenient way to use not up-to-date packages in R?
... R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) I was able to install the packages by: 1)Downloading Package Source from Package Archive 2)Installing the tar.gz from R Studio; Tools --> ...
written 4 months ago by yussab10
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Comment: C: There is a convenient way to use not up-to-date packages in R?
... I tried to install the packages but nothing changed. Furthermore the packages are loaded when: library(InSilicoDb). I can't figure out what is the problem, the main difference that I noticed is that you're using miniconda3... ...
written 4 months ago by yussab10
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Comment: C: There is a convenient way to use not up-to-date packages in R?
... > sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 ...
written 4 months ago by yussab10
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Comment: C: There is a convenient way to use not up-to-date packages in R?
... 1) thank you very much , I followed your instruction and now i don't have any Rtools WARNING on my Windows machine 2) I also have a Linux Machine with Ubuntu 20.04 and R version 3.6.3. > install.packages('https://www.bioconductor.org/packages/2.13/bioc/src/contrib/inSilicoDb_1.10.1.tar.gz') Insta ...
written 4 months ago by yussab10

Latest awards to yussab

Scholar 4 months ago, created an answer that has been accepted. For A: There is a convenient way to use not up-to-date packages in R?
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.

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