User: newscient

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newscient10
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Posts by newscient

<prev • 29 results • page 1 of 3 • next >
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mapToTranscripts() with + and - strand regions
... Hi, Anyone that has been using mapToTranscripts() method from genomicFeatures package and can explain to me the following. I am using it to extract relative position of each position in b within a regions. As: > res <- as.tibble( mapToTranscripts( b.gr,a.gr,ignore.strand=F)) I have a b.gr se ...
genome R genomicfeatures written 4 days ago by newscient10
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bigWigSummary with bed file for a specific amount of datapoints in output
... Hi , I am trying to use the bigWigSummary tool from UCSC (https://genome.ucsc.edu/goldenpath/help/bigWig.html) which can extract summary information for your bigwig files. The functionality seems pretty straight forward : bigWigSummary - Extract summary information from a bigWig file. us ...
ucsc mean summary average bigwig bed written 4 weeks ago by newscient10 • updated 4 weeks ago by Devon Ryan88k
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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 3 months 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 4 months 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 4 months 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 4 months 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 4 months 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 4 months ago by newscient10 • updated 4 months ago by Nicolas Rosewick7.3k
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Comment: C: Simulation of single-end reads from reference genome
... Sampling reads using a uniform distribution sounds better !? ...
written 14 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 14 months ago by newscient10

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