User: r.tor

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r.tor40
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5 days, 2 hours ago
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2 years, 4 months ago
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Posts by r.tor

<prev • 20 results • page 1 of 2 • next >
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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 weeks 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 5 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 5 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 5 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 5 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 5 months ago by r.tor40 • updated 5 months ago by WouterDeCoster39k
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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 6 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 6 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 6 months ago by r.tor40 • updated 6 months ago by bernatgel1.9k
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Comment: C: Sequence alignment algorithm for big size genes in MATLAB
... I use the "sequence alignment application" of Matlab Biology package to perform a global alignment. The query is the whole sequence of a gene from hg19 coordinate and the subject is the sequence of the same gene from NG RefSeq coordinate. I am gonna match both to identify the coordinate of each nucl ...
written 2.1 years ago by r.tor40

Latest awards to r.tor

Student 5 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 2.4 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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