User: Gyan Prakash Mishra

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Posts by Gyan Prakash Mishra

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Comment: C: Design matrix: DESeq2
... Thanks Michael for reply ! Yes I understood that it would be difficult to model batch and group since it is nested. so I guess using only ~group in design should take care of variance and depth across the sample. I did pca analysis using vst, I think its the sample looks fine here. please comment ...
written 10 weeks ago by Gyan Prakash Mishra0
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Design matrix: DESeq2
... Hi all, I have 20 samples, four genotype , three stimulation with two replicate each sequenced in two batch please see below table. coldata <- data.frame(row.names=colnames(countdata),genotype,Rep,stimulation,batch) coldata$group<- factor(paste0(coldata$stimulation,"_",coldata$geno ...
deseq2 written 10 weeks ago by Gyan Prakash Mishra0
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Comment: C: DESeq2: DESeq2 interaction term study result interpretation
... Thanks Michael !  Sorry I didn't read it carefully ! Now I understood why its so. It was really helpful !   ...
written 7 months ago by Gyan Prakash Mishra0
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DESeq2: DESeq2 interaction term study result interpretation
... Hi, I have RNAseq data from two conditions in two different genotypes. I have put the same design as explained in mannual of ?results. I am interested to know the effect of condition between two different genotype. Below is the code that i followed > condition <- factor(c(rep("Uns",4),rep ...
deseq2 written 7 months ago by Gyan Prakash Mishra0 • updated 7 months ago by Michael Love23k
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Comment: C: count table generation using summarizeOverlaps
... Thanks Martin I got my answer, gtf is not from same build. ...
written 2.9 years ago by Gyan Prakash Mishra0
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count table generation using summarizeOverlaps
... Hi, I am using DESeq2 to analyze RNA-seq data In this first step to generate count table I used following code. library( "GenomicFeatures" ) hse <- makeTxDbFromGFF( "Mus_musculus.GRCm38.84.chr.gtf", format="gtf" ) exonsByGene <- exonsBy( hse, by="gene") fls <- list.files( "Bamfiles", ...
deseq2 tutorial written 2.9 years ago by Gyan Prakash Mishra0
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Comment: C: significance of ChIPseq peak overlap
... I tried to reproduce the same but I am getting different p and p.adjust values   qSample tSample qLen  tLen N_OL   pvalue p.adjust ARmo_1nM GSM1174480_ARmo_0M_peaks.bed.gz GSM1174481_ARmo_1nM_peaks.bed.gz 812 2296   26 0.000999001 0.001998 ...
written 2.9 years ago by Gyan Prakash Mishra0
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Comment: C: significance of ChIPseq peak overlap
... Oh  sorry about that. I add that additional column manually. Here is the exact output.   qSample tSample qLen tLen N_OL pvalue p.adjust 1 TF1_peaks.bed Irf1_0.peaks.bed 13094 17119 2633 0.00009999 0.00009999 2 TF1_peaks.bed ...
written 2.9 years ago by Gyan Prakash Mishra0
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significance of ChIPseq peak overlap
... Hi, I am using enrichPeakOverlap of ChIPseeker to find significance of peak overlap. Here is my result of the overlap with no. of shuffle i.e nshuffle=10000 qSample tSample qLen tLen N_OL   pvalue p.adjust TF1_peaks.bed Irf1_0.peaks.bed 13094 17119 ...
chipseeker written 2.9 years ago by Gyan Prakash Mishra0 • updated 2.9 years ago by Guangchuang Yu1.1k
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p value for correlation of two bed files
... Hi all, I am comparing two CHIPseq peak bed file by checking overlap and calculating correlation value.suppose if  X coordinates of A overlaps with B then correlation would be X/total coordinates in A. In order to assess if  correlation is significant or not  I think P value is needed. so If anybod ...
chipseq written 3.6 years ago by Gyan Prakash Mishra0

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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Analysis of peaks generated from Homer using Diffbind

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