User: blur

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blur120
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120
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European Union
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5 years, 5 months ago
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b***@pazcorp.com

Posts by blur

<prev • 138 results • page 1 of 14 • next >
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Finding regulatory or structural elements
... 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 ...
chip-seq structural elements written 1 day ago by blur120 • updated 1 day ago by Papyrus320
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How do I learn to do ribo_seq the right way?
... 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 ...
ribo seq written 12 days ago by blur120
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Answer: A: Centrimo from the MEME-suit --neg option
... 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 blur120
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Centrimo from the MEME-suit --neg option
... 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 ...
meme centrimo neg written 22 days ago by blur120
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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 blur120
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Comment: C: peak summit in macs not the highest point
... Thank you for this thorough reply! I will do as you suggested :) ...
written 4 weeks ago by blur120
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Comment: C: peak summit in macs not the highest point
... Is the summit file not actually a list of peak summits? or is the IGV view not accurate? ...
written 4 weeks ago by blur120
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Comment: C: peak summit in macs not the highest point
... 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 blur120
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peak summit in macs not the highest point
... 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 ...
macs peak summit written 4 weeks ago by blur120
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Answer: A: How can get overlap size in bedtools multi-intersect?
... Perhaps I'm being slow, but don't see how this will apply to more than 2 files? ...
written 7 weeks ago by blur120

Latest awards to blur

Popular Question 8 days ago, created a question with more than 1,000 views. For UCSC peak calling - weird results
Popular Question 8 days ago, created a question with more than 1,000 views. For Bcftools magic string
Popular Question 23 days ago, created a question with more than 1,000 views. For UCSC peak calling - weird results
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Bcftools magic string
Popular Question 6 weeks ago, created a question with more than 1,000 views. For cutadapt --cut option for paired-end reads?
Great Question 4 months ago, created a question with more than 5,000 views. For Generate consensus from BAM file
Popular Question 4 months ago, created a question with more than 1,000 views. For cutadapt --cut option for paired-end reads?
Popular Question 4 months ago, created a question with more than 1,000 views. For Bcftools magic string
Popular Question 4 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
Popular Question 4 months ago, created a question with more than 1,000 views. For bcftools soft filters (-s)
Popular Question 11 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
Popular Question 11 months ago, created a question with more than 1,000 views. For MACS2 and duplicates
Popular Question 11 months ago, created a question with more than 1,000 views. For bcftools soft filters (-s)
Popular Question 11 months ago, created a question with more than 1,000 views. For fastq_quality_trimmer: Premature End-Of-File
Popular Question 16 months ago, created a question with more than 1,000 views. For Generate consensus from BAM file
Popular Question 16 months ago, created a question with more than 1,000 views. For uneven paired end reads in bowtie
Popular Question 16 months ago, created a question with more than 1,000 views. For BWA vs. bowtie
Popular Question 16 months ago, created a question with more than 1,000 views. For cutadapt --cut option for paired-end reads?
Popular Question 16 months ago, created a question with more than 1,000 views. For MACS2 and duplicates
Popular Question 16 months ago, created a question with more than 1,000 views. For FASTX error - quality score
Popular Question 19 months ago, created a question with more than 1,000 views. For The bed12 format
Popular Question 19 months ago, created a question with more than 1,000 views. For Bam to WIG
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Popular Question 20 months ago, created a question with more than 1,000 views. For The bed12 format
Popular Question 23 months ago, created a question with more than 1,000 views. For trim galore putfiles

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