User: newscient

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newscient10
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Posts by newscient

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Comment: C: Simulation of single-end reads from reference genome
... Sampling reads using a uniform distribution sounds better !? ...
written 12 weeks ago by newscient10
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Simulation of single-end reads from reference genome
... Hi, I am trying to simulate single-end sequencing reads from a reference genome but **uniformly distributed**. I have the desired read length and number of reads, I could easily use DWMSIM (https://github.com/nh13/DWGSIM) to generate reads randomly, but i am looking for a tool that would make things ...
reads simulation written 12 weeks ago by newscient10
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Comment: C: Histogram showing overlap between 2 bed files
... Could you provide the R code for getting such a mean depth of coverage graph out of the bed file generated by bedtools -coverage? ...
written 3 months ago by newscient10
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Histogram showing overlap between 2 bed files
... I'm trying to plot the counts of the overlap of the regions of 1 bed file on the regions of another bed file (the second file has same width regions in different parts of the genome) in a histogram like plot in base pair resolution. But what ever I have tried (using bedtools/bedops - binning,countin ...
overlap histogram written 3 months ago by newscient10
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Comprehensive gene annotation for drosophila melanogaster
... Is there a trustworthy and so-called comprehensive annotation for drosophila melanogaster of all genomic regions in order to construct a TSS (transcription start site) database? Is it UCSC (by quering), modENCODE, flybase or ensembl that i should search for it? I am looking for something like the G ...
genome written 7 months ago by newscient10 • updated 7 months ago by Jean-Karim Heriche14k
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Comment: C: Homology percentage for different species query
... You are right and i clarify. So i am not talking about the sequence similarity neither.When i am saying "homology percentage" , i mean the ratio : protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism. x 100 :-) ...
written 2.9 years ago by newscient10
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Homology ratio comparison between different species
... I found the homology ratio* for all protein coding genes between several organisms and mouse using a phylogenetic-based approach. I have noticed that the ratio found between an organism and mouse is greater than the ratio between another organism and mouse! On the other hand the second is evolutiona ...
homology evolutionary distance written 2.9 years ago by newscient10
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Comment: C: How to get gene names from CpG islands coordinates with R/Bioconductor
... I guess i have to make a mapping of my CpG coordinates with a mouse gene annotation, that's what i am missing, right? And then find the gene_ids from there! ...
written 2.9 years ago by newscient10
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How to get gene names from CpG islands coordinates with R/Bioconductor
... I have a dataframe with chromosome name , start position, end position (only! no other identifier) of CpG islands from the mouse genome (mm10 coordinates).  Is there a function with which i can retrieve the related ensembl gene ids? I suppose getBM from the bioMart package would do the job , but ho ...
annotation cpg written 2.9 years ago by newscient10 • updated 2.9 years ago by Martin Morgan1.5k
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Comment: C: True/False Positives/Negatives in R
... Yes your point about the control dataset is totally correct! But the genes "without peaks" will be the rest of the organism's genes which i also find meaningless, so i will stick with the discarded ones! Thanks again ...
written 2.9 years ago by newscient10

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Homology ratio comparison between different species
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Homology ratio comparison between different species
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to get gene names from CpG islands coordinates with R/Bioconductor
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Iterate over Rangeddata in R with a for loop
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to write a list of DNAStringsets as a FASTA file in R
Popular Question 2.9 years ago, created a question with more than 1,000 views. For True/False Positives/Negatives in R

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