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User: iraia.munoa

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iraia.munoa • 100
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Posts by iraia.munoa

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Problems with readBismark2DGE when uploading data
... Thanks!!!!! That solved my problem!!! ...
written 11 days ago by iraia.munoa • 100
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Comment: C: Problems with readBismark2DGE when uploading data
... 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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Problems with readBismark2DGE when uploading data
... 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 ...
bisulfite sequencing edger written 12 days ago by iraia.munoa • 100
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From Bismark to methylkit, which file is better to use?
... 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 ...
bisulfite sequencing bismark methylkit written 7 weeks ago by iraia.munoa • 100
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Answer: A: HISAT2 indexes, GRCm38 or mm10?
... 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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Comment: A: Bisulfite Analysis With Illumina Fastq From Different Lanes
... 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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Comment: C: output TMM normalized counts with edgeR
... ...
written 20 months ago by iraia.munoa • 100
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CPM plot for individual genes
... 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 ...
cpm rna-seq edger tmm written 20 months ago by iraia.munoa • 100 • updated 20 months ago by ATpoint ♦ 44k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Different results when visualizing tdf files in IGV and when doing the differential expression analysis with ballgown
Popular Question 7 months ago, created a question with more than 1,000 views. For Different results when visualizing tdf files in IGV and when doing the differential expression analysis with ballgown
Popular Question 7 months ago, created a question with more than 1,000 views. For Different options tryed with DiffBind and did not know what final result believe
Appreciated 19 months ago, created a post with more than 5 votes. For How to see if adjusting batch effect in RNA-seq is working or not
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For How to see if adjusting batch effect in RNA-seq is working or not
Popular Question 19 months ago, created a question with more than 1,000 views. For How to see if adjusting batch effect in RNA-seq is working or not
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Student 2.0 years ago, asked a question with at least 3 up-votes. For How to see if adjusting batch effect in RNA-seq is working or not
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