User: Zee_S

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Zee_S20
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Posts by Zee_S

<prev • 34 results • page 1 of 4 • next >
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How to correlate chip seq peaks?
... Hello everyone, I am seeking some tips on how to calculate the pearson/spearman correlation between two chip seq peak profiles. I have the coordinates of the peaks in a bed format. I think I have to bin the peaks and correlate the read count in aligned bins but I'm wandering, how to make sure the ...
pearson peaks correlation chip seq spearman written 16 days ago by Zee_S20 • updated 6 days ago by Rory Stark460
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how to correlate RNAseq dataset to chipset dataset?
... Hello, Can anyone please suggest me a method to look at the correlation between a chIP-seq dataset and RNA-seq dataset? Thank You very much! ...
rnaseq chipseq correlation written 11 weeks ago by Zee_S20
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how to produce a cluster plot of rna-seq + chipseq data?
... Hello everyone, I would like to create a correlation plot of some RNAseq data and ChIPseq data, would you happen to have any ideas on a good pipeline to do this, and what kind of normalization need to be done beforehand? I just want do a cluster analyses of the two datasets instead of using gene ...
rnaseq chipseq correlation written 11 weeks ago by Zee_S20
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Comment: C: How to do correlation analyses between RNAseq and ChIPseq library?
... yes, and if you get rid of those zero reads bins, you are essentially getting rid of any potential negative correlation with your chip seq data that you were looking for in the first place. or am I wrong on this point? ...
written 11 weeks ago by Zee_S20
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Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
... thanks, Colin. looks like a good tool to just look at coverage alone. multibam summary can indeed handle multiple bam files, thats not the problem. I just do not comprehend how it would be informative for correlating two (or more) bam files if they are not normalized for read count. ...
written 11 weeks ago by Zee_S20
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Comment: C: How to do correlation analyses between RNAseq and ChIPseq library?
... Hi Hussain, Thanks a lot for your reply. Could you kindly elaborate on the two approaches you mention above? (1) a larger value such as? And how does this solve the issue of zero reads bins in rnaseq dataset being included in the correlation? (2) what do you mean by absolute value? Thank you ...
written 12 weeks ago by Zee_S20
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Can one artificially increase read count per genomic bin for IP and Input libraries in order to prevent significant changes in log2ratio?
... Hello everyone! I was wandering about a very basic yet fundamental question related to chIP Input and IP library normalization. In a situation where the scaled read coverage per genomic bin for IP and Input libraries is low (e.g. on average 5 reads per bin), adding a pseudocount of +1 (for example ...
normalization chip-seq written 12 weeks ago by Zee_S20
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How to do correlation analyses between RNAseq and ChIPseq library?
... Hello Biostars community, I would be grateful to get your ideas on a pipeline to correlate the reads of a RNAseq dataset to chipset dataset? I have read many posts where one can calculate the counts per million (CPM) per genomic bin and correlate the two. But I have two questions regarding this app ...
chip-seq correlation rna-seq normalization written 12 weeks ago by Zee_S20 • updated 12 weeks ago by Hussain Ather880
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Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
... Hello Colin, Thanks a lot of your reply. I looked at the link you sent me.. thank you! It looks like the tool mentioned here for correlation is the deep tools multibamsummary tool followed by plot correlation tool. I am wandering if this tool normalizes the bam files for sequencing depth or library ...
written 12 weeks ago by Zee_S20
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Pearson correlation between chIP-seq replicates is very poor- am I doing something wrong in the normalization?!
... Hello everyone! I have several chIP-seq samples and their respective inputs and I want to find the Pearson correlation between different chIp replicates. I have read many posts and documentation about using deeptools, bedtools etc..for this purpose but for some reason, my correlation values are w ...
pearson correlation chip-seq written 12 weeks ago by Zee_S20 • updated 12 weeks ago by jomo018330

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