User: BenHu

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BenHu0
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Posts by BenHu

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how to analyze and recapitulate a public scRNA-seq data
... I downloaded a public scRNA-seq data, and try to reanalyze it using Seurat. however, I can not recapitulate the published results. does anyone have any suugestion? thanks in advance! ...
rna-seq written 4 weeks ago by BenHu0
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Answer: A: how to define cis regulatory elements using histone modifications ChIPseq
... I really appreciate you. I found that some literatures that reported H3K27ac peaks being broad. *These histone (modifications) carrying these marks are flanking nucleosome-free regions (what you see in ATAC-seq) therefore you (in many cases) should probably see quite an overlap between ATAC-seq an ...
written 9 weeks ago by BenHu0
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how to define cis regulatory elements using histone modifications ChIPseq
... Hello, I have some questions about Histone modifications ChIPseq. 1: why are H3K27ac peaks broad? 2: People use H3K27ac or H3K4me1 peaks to define enhancers. I thought enhancers and promoters are open chromatin regions which are Neucleosome Fragment Regions. Why do we use H3K27ac or H3K4me1 to d ...
chip-seq written 9 weeks ago by BenHu0
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Comment: C: CTCF motif orientation
... gotcha I really appreciate your help. ...
written 4 months ago by BenHu0
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Comment: C: CTCF motif orientation
... yeah. one paper used FIMO to analyze CTCF motif. But I do not understand how FIMO analyze orientation of CTCF motifs. ...
written 4 months ago by BenHu0
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Comment: C: motif for TF within CTCF boundary
... Hi, How to determine the TAD boundary? ...
written 4 months ago by BenHu0
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CTCF motif orientation
... Hello, I have analyzed CTCF ChIP-seq. Now I want to get the orientations for those CTCF peaks, And I also want to get convergent oriented CTCF peaks. Best, ...
chip-seq written 4 months ago by BenHu0
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Comment: C: Get MACs2 peaks associated with specific genes
... for homer: you just provide the coordinates of peaks. for MEME, you should extract fasta sequences with customer script or bedtools. for proximal targets: actually, you should use H3K27ac and H3K4me3, or other histone modification markers ChIP-seq data to define potential promoter and enhancers, or ...
written 10 months ago by BenHu0
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Comment: C: co-expression analysis from a scRNA-seq data
... if I know how to do that, I wouldn't ask this question. ...
written 12 months ago by BenHu0
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co-expression analysis from a scRNA-seq data
... I have downloaded a public expression matrix for a scRNA-seq. Does anyone know how to perform Gene-Gene Co-expression, like this paper Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain. Best, ...
rna-seq written 12 months ago by BenHu0 • updated 12 months ago by Kevin Blighe67k

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Popular Question 25 days ago, created a question with more than 1,000 views. For co-expression analysis from a scRNA-seq data

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