User: bioinfo

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Posts by bioinfo

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Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... By the way, when ChIP-seq data is analyzed by DESeq2 for differential binding (for example: diffBind), the region is pre-defined by peak calling software such as MACS. Here, the size of region is variable. If read depth is not good for DESeq2, do you think that small size of region is also not good ...
written 11 days ago by bioinfo0
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Comment: C: DESeq2: possible to compare read counts at single nucleotide level ?
... Thanks for your help !! ...
written 13 days ago by bioinfo0
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Comment: C: Differential ChIP-seq analysis
... Thanks for your answer ! ...
written 13 days ago by bioinfo0
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Comment: C: Differential ChIP-seq analysis
... Thanks for your answer. It is much clearer now to me. By the way, in the website you mentioned, I cannot read math notation in the wrapping up remarks probably due to browser formatting. Can you check it? ...
written 13 days ago by bioinfo0
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Differential ChIP-seq analysis
... I would like to compare two conditions with each two ChIP-seq (H3K27me3) samples. I searched for tools for differential binding and found that many including diffbind and csaw compares two conditions with read counts from pull down library only, not using input/control library/read count. The csaw h ...
diffbind csaw written 13 days ago by bioinfo0 • updated 13 days ago by Rory Stark2.5k
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DESeq2: possible to compare read counts at single nucleotide level ?
... Hi, I have some candidate genomic regions of interest and would like to see if they are differentially expressed between two conditions. Each condition has three biological replicates. Because I cannot define the boundaries of the candidate genomic regions exactly (they are not annotated with gene ...
rnaseq deseq2 written 13 days ago by bioinfo0 • updated 7 days ago by Gordon Smyth34k
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Comment: C: Few significance in DESeq2
... Thanks for your help. I agree with you. I don't want to do post-processing the p-values to have significance. I can conclude that they do not have significant genes. But it is still unclear that why the distribution of p-value is not flat in the case of no significant gene. If I understand you corre ...
written 8 weeks ago by bioinfo0
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Comment: C: Few significance in DESeq2
... Hi Michael, Thanks for your answer. You are right. In PCA plot, the samples are intermingled regardless of conditions. I understand that there are few significant genes in this case. However, while I expect that the distribution of p-value is almost flat in the case, I currently have some depletion ...
written 9 weeks ago by bioinfo0
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Few significance in DESeq2
... Hi I am comparing RNA-seq between two conditions (WT vs. KO) using DESeq2. I have two different distribution of p-values depending on the cut-off for genes based on counting and application of fdrtool. I would like to listen to your advice for which is a correct way to go. I used the following code ...
deseq2 written 9 weeks ago by bioinfo0 • updated 9 weeks ago by Michael Love18k

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