User: iraia.munoa
iraia.munoa • 100
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Posts by iraia.munoa
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... Thanks!!!!! That solved my problem!!! ...
written 11 days ago by
iraia.munoa • 100
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... sorry that variable name was wrong! I have changed the text to show it proprerly. Thanks! ...
written 12 days ago by
iraia.munoa • 100
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... Hi!
I am trying to analize some bisulfite sequencing data with edgeR after Bismark alingment and further steps.
On the begining I am having some problems with the readBismark2DGE function. I will write the Rscript here:
library("edgeR")
targets<-read.delim("targets.txt)
tar ...
written 12 days ago by
iraia.munoa • 100
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... Hi!
I am trying to analyse some Bisulfite sequencing data files, but I am new to this sequencing analysis mode and I am a bit stuck.
I have followed Bismark protocol for the alingment, deduplication and methylation extractor steps. And I am trying to follow the methylkit protocol. I have tried uploa ...
written 7 weeks ago by
iraia.munoa • 100
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... Hi everyone,
I add here my question, because it is about both GRCm38 and mm10 reference genomes.
I have received the fastq files of some Bisulfite sequencing samples. For the sequencing they have used "gem3.mmusculus.GRCm38_BS" as a reference. But I am not sure what genome to use for the analysis ...
written 8 months ago by
iraia.munoa • 100
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... Hi to all,
Maybe I am late to add a summary question for this problem. I have received my fastq files of the bisulfite methylation sequencing
and I have 16 files (different lines) for each sample. So I was thinking in the better way to follow for the analysis 1) concatenate at the begining 2) or wa ...
written 9 months ago by
iraia.munoa • 100
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Comment:
C: CPM plot for individual genes
... Well thanks!!! I will try! ...
written 20 months ago by
iraia.munoa • 100
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Comment:
C: CPM plot for individual genes
... Well I have been reading the link you showed me, but I am a little bite confused and don't understand what I need to run in `edgeR`.
In the coments James Ashmore provides a cpm.DGEList function, do I need to run it like that? Or running `cpm(y, log=TRUE, lib.size=libsize, prior.count=2)` after the ` ...
written 20 months ago by
iraia.munoa • 100
• updated
20 months ago by
ATpoint ♦ 44k
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... Hi!
I am working with my DEGs list from `edgeR` with TMM normalization. I have seen in many publications that researches plot `log2(FPKM)` values for individual DEGs to show the statistical significance. Regarding this, I would like to know if it is posible to plot the `log2(CPM)` values of contro ...
written 20 months ago by
iraia.munoa • 100
• updated
20 months ago by
ATpoint ♦ 44k
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