User: srhic

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srhic40
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Posts by srhic

<prev • 46 results • page 2 of 5 • next >
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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 8 months ago by srhic40 • updated 8 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 9 months ago by srhic40
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Comment: C: Chip-Seq normalization between conditions
... Thanks, the samples are histone marks under three different treatment conditions. I just have the bigwig files output by deeptools. I will try to import them in R and make a count table. Will try and get back. ...
written 9 months ago by srhic40
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Chip-Seq normalization between conditions
... Hello, I have some chip-seq data for three different conditions for which I have plotted RPKM normalized counts around features of interest using deeptools. The plot clearly shows differences in chip-signal between the conditions but I am concerned about different levels of backgrounds between cond ...
deeptools chip-seq written 9 months ago by srhic40
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Any tools for nucleosome phasing analysis of ATAC-Seq data?
... Hello, Can anyone recommend any pipelines for performing nucleosome phasing analysis on ATAC-Seq data? I want to perform analysis similar to the one performed in this paper (figure 1f and 2b): https://www.nature.com/articles/s41586-019-1115-5 The only tool I have been able to find is called nucle ...
next-gen atac-seq nucleosome written 9 months ago by srhic40
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Comment: C: Treated technical replicates as biological replicates by mistake
... For the chip-seq experiments I am most concerned about, I had 2 true biological replicates which I wrongly treated as 4. ...
written 10 months ago by srhic40
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Comment: C: Treated technical replicates as biological replicates by mistake
... Hmm, thanks. Guess I will have to redo everything. The RNA-Seq experiments had 3 biological reps per condition and the chip-seq experiments had 2 biological reps per condition. By not merging technical reps I effectively treated them as 6 and 4 reps respectively. ...
written 10 months ago by srhic40
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Treated technical replicates as biological replicates by mistake
... Hello, I need some help deciding if I made some mistakes in my analysis and how I can correct them. I had a few sequencing experiments including chip-seq and rna-seq which were run on separate lanes. Based on what I have read online, it seems that the standard practice is to either concatenate the ...
chip-seq rna-seq written 10 months ago by srhic40 • updated 10 months ago by ATpoint46k
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Comment: C: Average bigwig files (not sum)
... Thanks. That looks perfect. ...
written 11 months ago by srhic40
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Average bigwig files (not sum)
... Hello, I have bigwig (RPKM) files of a chip-seq experiment for treatment and control conditions which I am trying to compare. I have 3 replicates for control and 5 replicates for treatment condition. To show the average difference in signal, I merged the replicates for each condition using ucsc big ...
chip-seq bigwig written 11 months ago by srhic40 • updated 11 months ago by ATpoint46k

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Average bigwig files (not sum)

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