User: florian.noack

gravatar for florian.noack
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Germany
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5 months, 4 weeks ago
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3 years, 6 months ago
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f************@crt-dresden.de

Posts by florian.noack

<prev • 12 results • page 1 of 2 • next >
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Quantitative comparison of two different ChIP-seq data from same conditions
... Hi everyone, I am quite new to the ChIP-seq business and wetlab scientist so sorry for the maybe stupid question. I analyse epigenetic changes during the differentiation from cell type A to cell type B and performed Chip-seq of two different marks (X and Y). I used SCIER + Diffbind to identified dif ...
chip-seq written 7 months ago by florian.noack20 • updated 6 months ago by sysbiocoder170
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Comment: C: Which statistical test to compare expression of subset of genes from two cell ty
... Thanks for the fast response. I have to say the data i get from the above mention approach make biological sense. Gene where i expect a change (because they are methylated for example) show a change whereas other genesets (for example 500 random genes) show nothing. The problems comes when I subgrou ...
written 15 months ago by florian.noack20
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Answer: A: Which statistical test to compare expression of subset of genes from two cell ty
... Thanks for the fast response. I have to say the data i get from the above mention approach make biological sense. Gene where i expect a change (because they are methylated for example) show a change whereas other genesets (for example 500 random genes) show nothing. The problems comes when I subgrou ...
written 15 months ago by florian.noack20
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Which statistical test to compare expression of subset of genes from two cell types
... Hi everyone, Iam a bit puzzled which statistical test I should use for my data. I have a subset of genes (based on methylation status of the promoter) and the expression data (FPKM) of two lineage related cell types (FACS from one animal). Question is if there is a difference between the expression ...
rna-seq statistics written 15 months ago by florian.noack20
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Calculate enrichment values of Chip-seq peaks for hierarchical clustering
... Hi everyone, I have Chip-seq samples + input controls (triplicate) for three different cell types. I want to study the changes of the Chip-seq samples between the three different cell types. I called already peaks using MACS2 and generated a global peak file (if a genomic regions pops up in at least ...
chip-seq written 21 months ago by florian.noack20 • updated 21 months ago by igor6.6k
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Bismark: bismark2bedGraph option to add trinucleotide context option
... Hi everybody, I just started to use Bismark and I love it. However I missing one option to add the trinucleotide context of cytosines which I analyse. Since Iam interested in both CpG as well as non CpG methylation this information would be great. I know "coverage 2cytosine" has this additional inf ...
bisulfite-sequencing bismark dna methylation written 2.2 years ago by florian.noack20
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Comment: C: Tool to compare whole genebody enrichment between different samples (MeDip-seq)
... Just tried deepTools and its a great tool, thanks a lot ! However one question. To generate bigwig files i use bamcompare with -b1 ab treated sample -b2 input control --ration substraction and --normalizeUsingRPKM . I do this for celltype A and celltype B. Iam now confused if the bigwig files of cel ...
written 2.4 years ago by florian.noack20
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Comment: C: Tool to compare whole genebody enrichment between different samples (MeDip-seq)
... Great I will check this. However a "simple" plot will not help that much since I would like to correlate the changes of average DNA methylation of the gene body with the gene expression of the corresponding gene (like they did in the paper mention above). ...
written 2.4 years ago by florian.noack20
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Tool to compare whole genebody enrichment between different samples (MeDip-seq)
... Hi everyone, I have some MeDip datasets and did already comparisions of my datasets based on peaksets (MACS2). However I would like to find out if there is a average increase/decrease in methylation of, for example, genebodys (and if yes which genes) between celltyp A and celltyp B (normalized by l ...
chip-seq sequencing written 2.4 years ago by florian.noack20 • updated 2.4 years ago by Devon Ryan84k
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Comment: A: Comparison of two MeDip data sets
... Sorry Iam still not sure which method I should use. Is the following pipeline correct if I want to identify differential methylated region between celltype A and celltype B (especially about 6 Iam not sure).   1. Call Peaks using MACS (for each cell type separately) 2. Merge the peak patterns 3. ...
written 2.6 years ago by florian.noack20

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Correlation MeDip-seq data with gene expression data

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