User: r.tor

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r.tor40
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Posts by r.tor

<prev • 21 results • page 1 of 3 • next >
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(Closed) The best PCR based approach to genotype up to a hundred SNPs in human.
... Hello! I am looking for an accurate customizable technique to genotype up to a hundred SNPs, a range from 50 to 100. The SNPs are known but are located in different genes. The experiment assumed to be applied on human samples. Also, when I was checking out some related commercial kits, I saw the ...
snp genotyping written 6 months ago by r.tor40
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Where to get population diversity information of GTEx database?
... Hello, I am looking for population types of individuals (like FIN, TSI, GBR, ...) in GTEx database since I am trying to perform Principal Component Analysis using EIGENSTRAT. I actually failed in finding this data from GTEx portal and the annotation files, while certainly there must be somewhere! ...
pca gtex rna-seq written 10 months ago by r.tor40
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How to generate a short sequence that does not align to the hg38?
... I would like to find a short sequence (25 bp) that does not match anywhere within Human Reference Genome (hg38/hg19) through R scripts. I am not sure if there is a quick solution to do what I am looking for. So, I guess it would be solve, if I can create a list of random 25 bp fragments and then do ...
R alignment written 13 months ago by r.tor40
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Comment: C: Create snakefile based on R script
... just downloading the ordered regions from database! ...
written 13 months ago by r.tor40
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Comment: C: Create snakefile based on R script
... Hi, you mean is to put all R scripts in one rule? and what about the input section of the rule? ...
written 13 months ago by r.tor40
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Comment: C: Create snakefile based on R script
... Thank you for the reply. I want to make a workflow as Snakefile looking at my R scripts and yes it would be a begining part of workflow. I have just extracted the target regions considering the applied attributes and filters by getBM function in Biomart package. The source of all, is "hsapiens gene ...
written 13 months ago by r.tor40
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Create snakefile based on R script
... I have extracted the Transcription Start Sites (TSS) from hsapiens gene ensembl database and TSS flnaking regions through [biomaRt][1] and [GenomicRanges][2]. Then all targeted data has been stored in a bed format file. The code looks like this: library(biomaRt) library(regioneR) librar ...
R python snakemake snakefile written 13 months ago by r.tor40 • updated 13 months ago by WouterDeCoster43k
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Comment: C: Extracting Flanking Regions across TSS using R scripts
... Thank you so much! it helped me a lot. The code worked well after a minor modifications. And as you've mentioned, the next would be considering the overlapping regions. So, I'm wondering about merging all sequences to get an understandable result. I think that I won't need the sequences and it would ...
written 14 months ago by r.tor40
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Comment: C: Extracting Flanking Regions across TSS using R scripts
... Thank you for your answer and the tip! actually I didn't get the way to present the list of TSS to a GRanges object. I have a list of TSS coordinates that has been retrieved by the query like this: mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) att <- listAttribu ...
written 14 months ago by r.tor40
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Extracting Flanking Regions across TSS using R scripts
... Hi, Using [biomaRt][1] package in R, I have extracted the Transcription Start/Stop Sites of protein coding genes in human genome. So, I have a huge list of TSS. The next step is to get sequences of 1000 bp region upstream and downstream of retrieved TSS coordinates. I figured out that there isn't a ...
R bioconductor tss coding ensembl written 14 months ago by r.tor40 • updated 14 months ago by bernatgel2.4k

Latest awards to r.tor

Popular Question 6 months ago, created a question with more than 1,000 views. For What is the appropriate approach for CNV and loss of heterozygosity analysis?
Student 13 months ago, asked a question with at least 3 up-votes. For How to generate a short sequence that does not align to the RefSeq?
Scholar 3.0 years ago, created an answer that has been accepted. For A: What is the difference between using genome build hg18 and hg19 in Genome-wide S

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