User: srhic

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srhic30
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Posts by srhic

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Comment: C: Non-uniform p-value histogram in differential analysis
... Thanks, this is exactly what my histograms looks like. Do you think the FDRtools approach they use in the tutorial is something worth trying? (as I am not sure how ChIP-seq count data differs from RNA-Seq count data) ...
written 2 days ago by srhic30
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Comment: C: Non-uniform p-value histogram in differential analysis
... Thanks, I will try DiffBind as well. Also just to clarify my histograms are similar to D in the linked article but not exactly like it. I am having some trouble posting pictures but they are upward sloping with abundance of high p values but without a spike at 1. ...
written 2 days ago by srhic30
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Non-uniform p-value histogram in differential analysis
... I am analyzing chip-seq data for several DNA binding proteins and doing differential binding analysis between two different conditions. I am using HOMER for differential analysis which basically uses the standard Deseq2 pipeline to compare counts between peak regions. Using mac2 gives me ~20,000 pea ...
chip-seq rna-seq written 2 days ago by srhic30 • updated 2 days ago by rpolicastro3.2k
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Chip-seq data with low enrichment
... Hello, I am working with some chip-seq data for a broad epigenetic mark and want to perform some peak calling analysis. From some initial qc analysis based on deeptools fingerprint plots, it seems my chip efficiency was not very good and there is a lot of background (but I have also read that this ...
chip-seq written 10 days ago by srhic30
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Comment: C: Tn5 bias in atac-seq
... Thats a good idea. Thanks ...
written 3 months ago by srhic30
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Comment: C: Tn5 bias in atac-seq
... Thanks, I will try the chromVAR method. I also expect that accounting for Tn5 bias will not significantly change my results. Based on some quick reading it seems to me this is more of an issue in case of transcription factor footprinting or motif enrichment etc. Since all I have done is a simple dif ...
written 3 months ago by srhic30
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Tn5 bias in atac-seq
... Hello, I recently got back reviews for a paper that contained some atac-seq analysis. The paper followed a standard analysis pipeline where peak calling was done using macs followed by differential analysis between two samples using deseq2. One of the reviewers mentioned that we should include 'a ...
tn5 next-gen atac-seq written 3 months ago by srhic30
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Comment: C: ATAC-Seq: Filter bams for differential analysis or not
... Thanks. I want to do a general comparison between two mouse cell lines one of which is a control and the other lacks a chromatin remodeling protein. Can you explain why you think MACS2 peak calling and differential analysis will not be useful for a general analysis? I have seen some papers using mac ...
written 6 months ago by srhic30
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ATAC-Seq: Filter bams for differential analysis or not
... Hello, I am doing some analysis to identify differential accessible regions between two conditions using atac-seq. The workflow I have followed uses peak calling with macs2 and then differential analysis of these peaks with deseq2. This gave me good results with expected genes changing accessibili ...
atac-seq written 6 months ago by srhic30 • updated 6 months ago by Devon Ryan98k
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Comment: C: Chip-Seq normalization between conditions
... I am trying out quantile normalization the way you described it for atac-seq. I was also able to get some good results using HOMER. I divided the genome into windows with bedtools and then extracted counts for those windows using HOMER which has an option that allows the counts to be normalized usin ...
written 7 months ago by srhic30

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