User: bede.portz

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bede.portz450
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Posts by bede.portz

<prev • 55 results • page 1 of 6 • next >
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Answer: A: Are HOMER aggregate proflles normalized to the read depth of each ChIP-seq sampl
... Provide some more detail, please. Are you using annotatePeaks -hist ? If so, the default is to normalized the read files to 10,000,000 reads. See the link below and scroll to the bottom under the heading "advanced options." I hope this helps.    http://homer.salk.edu/homer/ngs/annotation.html ...
written 21 months ago by bede.portz450
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Comment: C: Plot of intergenomic distances between all bound TF sites?
... Alex, Thanks for the response. It appears from a cursory look at the documentation that closest features wants two input files, can I run it with just the one input file? I.e. the bound intervals for a given factor?  Thanks ...
written 2.0 years ago by bede.portz450
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Plot of intergenomic distances between all bound TF sites?
... I would like to plot the distance between all pairs of peaks/bound locations for a specific transcription factor. In other words, generate a histogram of inter-genomic distances between all bound locations. Essentially a composite plot of the data, but with the bound location being both the referenc ...
peaks chip-seq written 2.0 years ago by bede.portz450 • updated 2.0 years ago by Alex Reynolds21k
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Comment: C: why only small fraction of reads from control sample of chip-seq are mapping int
... What do you consider a small percentage? What, specifically, is the nature of the control? What genome?  ...
written 2.4 years ago by bede.portz450
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Answer: A: what is the motivation behind Pol2 chip-seq data?
... You write: However, RNA polymerase 2 is just a protein that transcribes genes. Why do we care about where it is (ie, where it is bound) at the moment chip-seq is run? The very point of histone modifications, transcription factor binding, the binding of pausing, elongation, and termination factors, ...
written 2.7 years ago by bede.portz450
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Answer: A: Clearly formed IgG Peaks in CLIP-Seq
... While I don't have CLIP-seq experience, I have ChIP-seq experience specifically using a protocol with inherently low background relative to other methodologies. In the absence of of any IgG, or with a pre-immune serum control, it is possible to see peaks. This is in essence the point of the no-IgG, ...
written 2.7 years ago by bede.portz450
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Answer: A: A new perspective needed for a newbie
... Being a scientist, and certainly becoming one, is a vocation, that is also at times very much a job.  What you are describing is simply the process of learning science, be it bioinformatics, or otherwise. When I joined my lab I had the help of senior graduate students, sometimes. Other times I was ...
written 2.8 years ago by bede.portz450
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Answer: A: Query related to generating plots from HOMER output
... AnnotatePeaks should be able to do this.  annotatePeaks peakfile1.bed genome -size # -hist # -noadj -d peakfile1.bed > output.txt Here the first peak file will be the reference against which the second peak file will be plotted against.  -size # is the area around the first peak file about wh ...
written 2.8 years ago by bede.portz450
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Answer: A: upscaling ChIP-seq data
... Homer may do what you need. If by "track" you are referring to a file you can visualize on the UCSC browser, IGV, etc, than you can take your reads and use homer to make a tag directory, then use homer to make a bedgraph. Homer defaults to 10million reads for each file, or "track," using the makeUCS ...
written 2.8 years ago by bede.portz450
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Comment: C: How to avoid problem using -size, -hist and -ghist for annotatePeaks.pl in HOMER
... Can you provide the specific command you attempted to use? ...
written 3.0 years ago by bede.portz450

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