User: shikhtechai

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Posts by shikhtechai

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Comment: C: lncRNA annotation for featureCouns and STAR
... Hi, I am having similar problem. Did you find any solution? ...
written 11 hours ago by shikhtechai0
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Comment: C: How to get all possible comparisons in DiffBind
... Hi Rory, I am having similar situation. If we take the example above. Then, to get all possible comparisons, I have to write code chunks, as following? #Lets assume "result=our DBA object having samples for multiple pairwise comparison" dba.count(result) # for counting the reads for a ...
written 3 months ago by shikhtechai0
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How to use ChIPseeker for getting genebody annotations.
... Hi, I would like to get the genes that have peaks in their genebody. Let's say, I have a ChIPseq data for a histone modification and after I did the annotation with chipseeker, how can I only select the genes that have histone modification of interest on their genebody? As later, I would like to do ...
chipseq chipseeker written 4 months ago by shikhtechai0
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Comment: C: How to do functional enrichment analysis for only promoter regions using ChIPsee
... That's what I was looking for. Thanks a lot! ...
written 7 months ago by shikhtechai0
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Comment: C: How to do functional enrichment analysis for only promoter regions using ChIPsee
... To clarify a bit, I wanted to do functional pathway analysis for my H3K4me3 peaks. Now, I want to take only the peaks that are present within +/-2000bp from TSS of genes. How can I select only those genes? I have followed your nicely compiled ChIPseeker tutorial page. But It does the pathway analysi ...
written 8 months ago by shikhtechai0
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
... I am trying to use ChIPseeker to annotate and do functional enrichment analysis for H3K4me3 peaks. I am a bit confused using seq2gene function. How can I only select those genes which has H3K4me3 peak in +/- 2000bp? From the tutorial, in the arguments, there's option for "tssRegion = c(-1000, 1000), ...
chipseq chipseeker written 8 months ago by shikhtechai0 • updated 7 months ago by Guangchuang Yu1.1k
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Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
... 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 ...
chipseq diffbind chipqc written 13 months ago by shikhtechai0 • updated 12 months ago by Rory Stark2.8k

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