User: svlachavas

gravatar for svlachavas
svlachavas450
Reputation:
450
Status:
Trusted
Location:
Greece
Website:
https://www.linkedin.c...
Last seen:
5 hours ago
Joined:
2 years, 10 months ago
Email:
s*********@eie.gr

Posts by svlachavas

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Download latest reference genome assembly for exome sequencing alignment and var
... Dear genomax, thank you for your information and comments- actually whole exome sequencing has been performed (Genomic DNA captured using Agilent in-solution enrichment methodology/paired-end 75 bases massively parallel sequencing on Illumina HiSeq4000) and i already have the fastq files. So, my n ...
written 3 days ago by svlachavas450
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Comment: C: Download latest reference genome assembly for exome sequencing alignment and var
... Thank you very much for your link ...
written 3 days ago by svlachavas450
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Comment: C: Download latest reference genome assembly for exome sequencing alignment and var
... Dear genomax, thank you for your alternative proposal-so, you would suggest for my purpose, the GENCODE reference assembly ? or there are some strengths on each source, that i would have to take into account ? ...
written 3 days ago by svlachavas450
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Download latest reference genome assembly for exome sequencing alignment and variant calling
... Dear Community, i would like to search and download the latest possible human reference genome assembly hg38/GRCh38, in order to use it both in the process of sequence alignment of raw reads, as also for variant calling concerning exome sequencing. However, I'm a bit confused about the available op ...
reference genome dna sequence alignment written 3 days ago by svlachavas450 • updated 3 days ago by WouterDeCoster29k
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Answer: A: Find Information about TCGA samples from GDC data portal
... Dear Ankita, consider that from my personal search and email one or two years ago, to the main contributors and directors of the TCGA project-which "evolved" to GDC, i got the following answer : "The criterion used for all of the TCGA projects, is that samples be obtained from the primary tumor sit ...
written 8 days ago by svlachavas450
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Answer: A: Subsetting a RangedSummarizedExperiment in R
... Dear Aluesley, firstly you have to be more specific of your type of analysis and target goals, as your description is rather confusing ? 1) So firstly, as you mentioned that you are a new user in R, you have to first familiarize a bit with "data containers" and basic workflows, as nicely included ...
written 10 days ago by svlachavas450
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Comment: C: dbSNP annotation database and appropriate filtering in somatic variant calling p
... Ok Kevin, got your point-we are actually using the CADD score through SnpSift, in order to select the most deleterious variants, so i guess through this context our approach is valid- nevertheless, i would also take a detailed look on the other specific programs that you have mentioned- ...
written 11 days ago by svlachavas450
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Comment: A: TCGAbiolinks TCGA-BRCA RNA-seq clinical data
... Dear Matina, what is your purpose with the RNA-Seq data ? DE analysis ? looking for example to inspect the expression of specific genes ? or looking for molecular subtype pattern and survival analysis ? i think you already got an answer from one of the creators of the R package in the github accoun ...
written 11 days ago by svlachavas450
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Comment: C: Differences between RTCGA and TCGAbiolinks data
... Dear atakanekiz, it is nice to hear that you processed your data and find possible solutions on this matter-just an additional comment, in case you haven't used or tried the function TCGAanalyze_SurvivalKM- i think that includes anything you searched, as also the TCGAanalyze_survival - Best, Efst ...
written 11 days ago by svlachavas450
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Comment: C: dbSNP annotation database and appropriate filtering in somatic variant calling p
... Dear Kevin,thanks for the update and also for the very useful link- a lot of tools included, as also some of these we are already implemented them in our pipeline- just also to mention one extra important thing: the aformentioned data I refer here, are exome sequencing data-so, the point of assess ...
written 12 days ago by svlachavas450

Latest awards to svlachavas

Teacher 11 days ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Voter 8 weeks ago, voted more than 100 times.
Centurion 10 weeks ago, created 100 posts.
Scholar 6 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 7 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Supporter 21 months ago, voted at least 25 times.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 2.8 years ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor

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