User: florian.noack

gravatar for florian.noack
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Germany
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3 weeks, 4 days ago
Joined:
3 years, 8 months ago
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f************@crt-dresden.de

Posts by florian.noack

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Remove specific number of identical reads from fastq or bam files
... Because its ChIP-seq and I would expect to have some duplicates simply because we reduce extremely genomic complexity especially in the case using just a few cells (additional lost of complexity simply by losing some DNA fragments after shearing). Iam not sure which exact number i will allow later i ...
written 6 weeks ago by florian.noack20
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Remove specific number of identical reads from fastq or bam files
... Hi, I dealing right now with some ChIP-seq data generated from a very low number of cells. Data look so far good but I noticed that some loci got heavily amplified during library preparations which is I guess a consequence of working with low amounts of material. I looking now for a tool to restric ...
duplicates chip-seq written 6 weeks ago by florian.noack20
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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 9 months ago by florian.noack20 • updated 9 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 17 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 17 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 17 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 24 months ago by florian.noack20 • updated 23 months ago by igor7.1k
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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 2.4 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 2.7 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 2.7 years ago by florian.noack20

Latest awards to florian.noack

Popular Question 8 months ago, created a question with more than 1,000 views. For Tool to compare whole genebody enrichment between different samples (MeDip-seq)
Popular Question 8 months ago, created a question with more than 1,000 views. For Correlation MeDip-seq data with gene expression data
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Correlation MeDip-seq data with gene expression data

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