User: blur
blur • 120
- Reputation:
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- European Union
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- 1 day, 3 hours ago
- Joined:
- 5 years, 5 months ago
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Posts by blur
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... Hi,
I have peaks that are expected to fall into areas outside genes, that might or might not have structural elements or a specific regulatory area.
The people doing the bench work don't know what to expect.
The question is - is there a smart way to check for such elements? A list of peaks will ...
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... Hi,
I want to do ribo seq analysis - I started out by trying to recreate the results of a paper I found, but got different numbers than the published data (I assume it's my fault and not the data itself). I keep getting low alignment rates that might be ruining everything...
So, basically, does any ...
written 12 days ago by
blur • 120
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... I figured it out!
When I ran the negative peaks on their own I was looking for the motifs that are in the negative peaks
When I ran the --neg option it takes the motifs that were *indicated in the positive peaks* and checked these *positive motifs* to see if they are enriched or depleted in the sam ...
written 16 days ago by
blur • 120
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... Hi,
I have peaks and negative peaks (i.e. I switched the IP and input files).
I ran centrimo individually on each file and got a list of motifs.
Now I used the centrimo --neg option to see how they plot against each other, to assess the motifs found and I got a different looking graph than what I e ...
written 22 days ago by
blur • 120
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Answer:
A: Finding motifs strategy
... You might want to try Homer - it will allow you to set a background set of sequences and that might help elucidate things
http://homer.ucsd.edu/homer/motif/ ...
written 26 days ago by
blur • 120
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... Thank you for this thorough reply! I will do as you suggested :) ...
written 4 weeks ago by
blur • 120
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... Is the summit file not actually a list of peak summits? or is the IGV view not accurate? ...
written 4 weeks ago by
blur • 120
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... my files are bam files, created by:
alignment to reference using bwa (creating sam files)
Then by samtools view -bS turned into bam files
then sorted using samtools sort ...
written 4 weeks ago by
blur • 120
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... Hi,
I ran macs on my files and took out the peak summits for further analysis.
But then I opened my files in IGV, and the position of the summit does not look like the highest point in the peak.
I ran the analysis again to make sure it was not some error I did, but got the same summits.
Anyone ha ...
written 4 weeks ago by
blur • 120
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... Perhaps I'm being slow, but don't see how this will apply to more than 2 files? ...
written 7 weeks ago by
blur • 120
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