User: dcwest

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dcwest0
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Posts by dcwest

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Answer: A: chipseq -- annotate peaks with lncRNA
... Hi there, my similar question is about how these regions are defined... Promoter regions make sense Downstream (<=3kb) Does <=3kb mean the entire three promoter subset regions? Distal Intergenic -- what defines this region? Is it >=3kb, or something even more distal, or just anything inter ...
written 3.4 years ago by dcwest0
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Comment: C: ChIP-Seq TSS Line Plot
... Would you mind sharing the code one can use to change the color scale on these types of plots in ChIPseeker? Thank you! ...
written 3.5 years ago by dcwest0
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Answer: A: a problem with peak annotation after ChIP-seq
... Hi gpdus67 and Rituriya, I'm not sure if this will help, but I had the same issue too--- I ended up needing to convert my .txt peak file from a Macs-based .txt file into an acceptable .txt file that annotate.pl could handle. So, in Homer, I did: changeNewLine.pl path/peakfile.txt I did this for ...
written 3.5 years ago by dcwest0
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Comment: C: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
... Hi there! Awesome program! I just started using it with VMWare on my Mac. I'm having a similar difficulty with this issue of Dataset vs. Regionset as well. I have MACS2-called ChIP-seq peaks (ChIPed a transcription factor) that have been called and then normalized to Vehicle control samples usin ...
written 3.6 years ago by dcwest0

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