User: r.tor

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r.tor40
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Posts by r.tor

<prev • 19 results • page 1 of 2 • next >
11
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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 4 weeks ago by r.tor40
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Comment: C: Create snakefile based on R script
... just downloading the ordered regions from database! ...
written 6 weeks 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 6 weeks 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 6 weeks 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 6 weeks ago by r.tor40 • updated 6 weeks ago by WouterDeCoster36k
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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 11 weeks 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 11 weeks 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 11 weeks ago by r.tor40 • updated 11 weeks ago by bernatgel1.7k
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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 21 months ago by r.tor40
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Comment: C: Sequence alignment algorithm for big size genes in MATLAB
... Thanks for the response. Is there any specific code or package that you may know that is able to deal with this issue which is optimized considering the memory or specific algorithm that you are familiar with. I would very appreciate if you can guide me. ...
written 21 months ago by r.tor40

Latest awards to r.tor

Student 4 weeks 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 2.0 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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