User: sikhtechai

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sikhtechai30
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Posts by sikhtechai

<prev • 7 results • page 1 of 1 • next >
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Comment: C: distanceToTSS different in HOMER and ChIPseeker annotation
... Makes sense. Thanks a lot! Also, I have one small question regarding this. After doing the annotation in ChIPseeker, I wanted to do Functional enrichment for the genes. Now, I want to only take the genes which has the ChIPseq peak(H3K4me3 in my case) around +/-2000bp around TSS. The tutorial says, ...
written 4 months ago by sikhtechai30
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distanceToTSS different in HOMER and ChIPseeker annotation
... I am comapring the annotations of HOMER and ChIPseeker. I am noticing, for a gene that is annotated by Homer, the DistanceToTSS is always higher in HOMER, compared to ChIPseeker. For example, I have a set of genes, where I am annotating H3K4me3 peaks. With Homer, I am getting the distance for those ...
chipseeker chip-seq written 4 months ago by sikhtechai30 • updated 4 months ago by jared.andrews071.7k
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Comment: C: Downsampling ChIP-seq BAM files with spike in normalization factor before feedin
... But technically, this will still be raw counts, just spike in adjusted for all samples. For RNA-seq, there are already a package ([Ruvseq][1]) which does this spike in normalization for the counts matrix, which can be used for DESeq2 analysis. [1]: https://bioconductor.org/packages/release/bioc ...
written 9 months ago by sikhtechai30
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Comment: C: ChIP-seq: Should we be consistent with the control used (IgG/Input) among differ
... Makes sense! Thank you very much! ...
written 9 months ago by sikhtechai30
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Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into differential binding analysis
... I am planning to use exogenous chromatin as a spike in control with my actual sample from mouse to perform ChIP-seq for peak calling and differential binding analysis for histone modifications. this involves down-sampling the uniquely mapped read files to the calculated normalization factor from the ...
csaw diffbind differential binding chip-seq written 9 months ago by sikhtechai30 • updated 9 months ago by nicolas.descostes130
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Comment: C: ChIP-seq: Should we be consistent with the control used (IgG/Input) among differ
... What about H3 ChIP-seq as control? As H3 gives nucleosome occupancy, do you think it might be more appropriate instead of Inputs? ...
written 9 months ago by sikhtechai30
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mm10 enhancer annotation for ngs.plot.r
... Hi! I have used ngs.plot for plotting ChIP-seq reads over promoter or genebodies. But I was interested to see the peak profile over enhancers. My reads are mapped to mm10 and for that, ngsplot doesn't have enhancer annotation. One solution I thought would be to remap on mm9 and reanalyze. Or, maybe ...
peak chip-seq visualization written 20 months ago by sikhtechai30 • updated 5 months ago by whm5680192400

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