User: christoph.neu

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Posts by christoph.neu

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Roadmap Epigenomics looks random
... Yes I do (because the data set from my lab is mm10 and this is what I had laying around), however this does not change the overall coverage of the roadmap data. The complete genome looks like this section. So even with the correct reference one would not see an enrichment at the TSS. ...
written 22 days ago by christoph.neu0
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Roadmap Epigenomics looks random
... Hello, I want to analyze the differences of histone peaks between cell types. For that i obtained some bed files from the [Roadmap Epigenomics][1] project. However the data looks highly unspecific and covers mostly everything. [Here][2] is an example file and where i got it from. For illustratio ...
chip-seq written 22 days ago by christoph.neu0 • updated 22 days ago by genomax85k
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Tool to find partial and complete Peak Intersection
... Hello, I have replications of a chipseq experiment. All have been processed and peak called. Now I want to combine those bed files that only areas which have a peak in at least X percent of the files are called. Is there a tool which has a feature like that? Example: A.bed: 1 5 20 ...
bed chip-seq written 22 days ago by christoph.neu0
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Comment: C: Correlation Plot for bed files
... works great, thanks a lot ...
written 5 weeks ago by christoph.neu0
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Comment: C: Correlation Plot for bed files
... thanks for the answer. However, I don't have a slurm cluster and running chromCor2 directly on starch or bed files gives me a dimension error for rds ...
written 5 weeks ago by christoph.neu0
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Correlation Plot for bed files
... Hey, I am looking for a tool, which calculates a correlation coefficient for a set of bed files. Preferably it would also provide a visualization for it. Similarly to what the combination of "multiBamSummary" and "plotCorrelation" from deeptool does for bam files. e.g. between all bedfiles from ...
bed visualization written 6 weeks ago by christoph.neu0 • updated 5 weeks ago by A. Domingues2.2k
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Answer: A: Segway Heat map of parameters
... For future reference (The segway mailing list helped out): > To generate heatmaps, you should use the segtools software suite > (https://hoffmanlab.org/proj/segtools/). Specifically you want to look > at the command, `segtools-gmtk-parameters`, which will generate > a heatmap of emissio ...
written 9 weeks ago by christoph.neu0
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Segway Heat map of parameters
... Hello, I want to discover chromatin patterns in ChipSeq data using [segway][1]. I followed the quick start instruction and trained a model on the test dataset. wget http://noble.gs.washington.edu/proj/segway/2011/test.genomedata segway train test.genomedata traindir segway identify tes ...
segway written 9 weeks ago by christoph.neu0
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Comment: C: Biomart mapping ensembl_transcript_id_version
... thanks, this way it works. ...
written 4 months ago by christoph.neu0
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Comment: C: Biomart mapping ensembl_transcript_id_version
... Thanks, then I will just use the no-Version approach. (Also, because I am not sure whether I use the tool you mention correctly. If I query for ENSMUST00000109424.2 , I get no results.) ...
written 4 months ago by christoph.neu0

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