User: chiefcat

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chiefcat70
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Posts by chiefcat

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Comment: C: ChIP-Seq identification of peaks
... Hi Kevin, thanks for the answer. Just wanna ask if MACS2 can perform reads per genome coverage [RPGC] normalization? ...
written 11 days ago by chiefcat70
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Comment: C: Doubts related to MACS tool
... Hi Pierre, Thanks very much for your detail explanation. For point 3) **"-P" is given because there are different ways of of normalization. You can normalize by RPM, RPGC ..."**, what should be set for the "-P" if I want to do the normalization by RPGC? Kylie ...
written 12 days ago by chiefcat70
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Are there any tools which can plot biclustered heatmap on ChIP-seq. signal?
... Hi all, It is very common to perform clustering analysis when plotting ChIP-seq. signal as a heatmap (e.g. around TSS) for finding regions having similar pattern across different samples. Are there any heatmap plotting tools which can do a biclustering, which allows finding regions having dissimila ...
chip-seq clustering heatmap written 16 days ago by chiefcat70
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Comment: C: [ChIP-seq. signal plot] How to merge ChIP-seq. biological replicates for signal
... Hi Devon, thanks for your reply. Should I scale them according to no. of reads? ...
written 24 days ago by chiefcat70
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Comment: C: [ChIP-seq. signal plot] How to align the based line of different samples?
... Thanks Devon. Yes, I also think it is dangourous to interpret the slight differences (I will try to convince my PI not doing that as well. I think it is much worth to spend time on searching real differences). By the way, do you mean using `--outFileNameData` to save the data underpaying the plot? ...
written 24 days ago by chiefcat70
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[ChIP-seq. signal plot] How to align the based line of different samples?
... Hi all, Does anyone have an idea how to make the baseline of different samples to the same level in a ChIP-seq. signal plot? I've been using deepTools for normalization and plotting (have tried different normalization method provided in deepTools e.g. 1x normalize, log2 ratio, SES normalization bu ...
deeptools chip-seq normalization written 24 days ago by chiefcat70 • updated 20 days ago by Dave Gerrard190
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[ChIP-seq. signal plot] How to merge ChIP-seq. biological replicates for signal profile plotting?
... Dear all, In ChIP-seq. analysis, what is the proper way to combine biological replicates for signal profile plotting? At the moment, I'm using deepTools `plotProfile` to visualize the signal density around TSS. After plotting the replicates separately, I can see that they are highly similar. Then, ...
deeptools biological replicates chip-seq written 24 days ago by chiefcat70 • updated 24 days ago by Devon Ryan75k
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Input control for ChIP-seq. [Seeking for the clarification between "Library DNA conc.", "no. of raw reads", and "normalization"]
... Hi all, Although the Input control is commonly used for in ChIP-seq. analysis (e.g. for normalization, as background for peak calling), it seems hard to find an easily understandable description explaining how it can be properly prepared (Before sequencing) and used in later data analysis stage. Wh ...
sample preperation normalization chip-seq written 4 weeks ago by chiefcat70 • updated 4 weeks ago by Carlo Yague3.6k
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[ChIPSeeker] Getting overlapping genomic feature annotation (e.g. peak locate in gene A & defined TSS region of gene B)
... Hi guys, I'm trying to use ChIPseeker but couldn't find a way to call the overlapping features during peak annotation. Example: TSS setting: -3kb +500bp --> I would like to get the ChIP peak annotated with "Rrs1, 3'UTR" & "Adhfe1, TSS" I've tried a lot of different arguments but all of t ...
annotation chipseeker chip-seq written 3 months ago by chiefcat70 • updated 3 months ago by Guangchuang Yu1.6k
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Comment: C: Sorting heatmaps by gene expression
... Hi Ryan, it's me again. When I performed `computeMatrixOperation` using the self-constructed matrices, a warning prompted out > chrom, start, end, name, score, strand = region[0:6] ValueError: not > enough values to unpack (expected 6, got 1) I think that there is something wrong during the ...
written 3 months ago by chiefcat70

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