User: newscient

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newscient10
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Posts by newscient

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Plot average expression profile from one bed file across overlapping regions fro
... As a newbie with tidyverse, i need to ask. Does this average TPM calculation take into consideration the length of b, where the expression measurements are taken from? I am just thinking that this way we don't actually get an average expression. imagine the case of getting one hit in one region in a ...
written 7 weeks ago by newscient10
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Comment: C: Plot average expression profile from one bed file across overlapping regions fro
... No, that's what i am referring to as a summarised average. In order for it to be meaningful these cases should be added up and divided by the number of counts observed (or just get the expression value from b.bed once) and then averaged across all the 400bps of the a.bed. But in any case I am intere ...
written 9 weeks ago by newscient10
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Comment: C: Plot average expression profile from one bed file across overlapping regions fro
... There are actually overlapping entries inside a.bed. (And there are several overlaps with b.bed, i just show the construct in the example above (answering to your comment in your response below)). But i can subset based on some annotation and have non-overlapping subsets. So you can consider that th ...
written 9 weeks ago by newscient10
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Comment: C: Genomic overlay plot in R
... Maybe I haven't explained it correctly I want to get summarised average expression/expression profile across the region of 400bp. In other words, I want to know where I get expression from b.bed across these 400 bp in a.bed and not on a chromosome basis. To visualise it: Check figure5 and 6 in this ...
written 9 weeks ago by newscient10
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Comment: A: Genomic overlay plot in R
... Thanks, but I was thinking of genome wide and not per chromosome resolution. As I said Average expression (y-axis) vs 400 bp region of the a.bed regions. Like a type of ChIP-seq signal over genomic region plot (e.g. some bp around a TSS). Any solutions? ...
written 9 weeks ago by newscient10
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Plot average expression profile from one bed file across overlapping regions from another bed file in R
... Hello, I have 2 bed files: one with standard length regions of 400 bp (a.bed) and one with Transcription start sites (TSS) of 1 bp length (b.bed), shown below. I want to overlay/overlap the two files taking into consideration strandness (same strands) and plot the average expression in tpm (column ...
bedtools bed R granges overlap written 9 weeks ago by newscient10 • updated 9 weeks ago by Nicolas Rosewick7.0k
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Comment: C: Simulation of single-end reads from reference genome
... Sampling reads using a uniform distribution sounds better !? ...
written 12 months 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 months 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 13 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 13 months ago by newscient10

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