User: rbronste

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rbronste290
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Posts by rbronste

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Retrieving count averages from a binding matrix
... I am interested in being able to retrieve count averages from a diffBind count matrix using a set of intervals, specifically to be able to limit my count average retrieval to specific columns in the count matrix of a set of unique intervals. Wondering if there are any good approaches to do that, tha ...
diffbind deseq2 chip-seq written 7 hours ago by rbronste290
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Comment: C: Color points on an Enhanced Volcano Plot based on external intervals
... Thanks for your input on this, so the bed file contains regions of interest from a different comparison that I want to map onto this particular Volcano Plot just to visualize distribution - discrete color scale would work well for this. My input data.frame is a DESeq2 result. Thanks again. ...
written 2 days ago by rbronste290
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Color points on an Enhanced Volcano Plot based on external intervals
... I was wondering whether there was a way to color points in an Enhanced Volcano Plot not based on the internal stats but just with a bed file input? Thanks. ...
plotting volcano plot written 2 days ago by rbronste290
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Comment: C: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' lengt
... Figure out a solution to this by chance? Getting similar error. ...
written 4 days ago by rbronste290
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Plotting range/type of discordance in alignment data
... I was wondering if there was a way, in a Bowtie2 output, to plot the range and type of discordance? The really obvious kind when two mates are on separate chromosomes, and more subtle types such as orientation and spacing specific discordance. Just trying to tease apart the unaligned and discordant ...
bowtie2 sequence alignment written 11 days ago by rbronste290
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Comment: C: multiple bed - merge regions IF overlapping more than xx percent of size
... Absolutely, exactly what I needed, thanks! ...
written 16 days ago by rbronste290
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Comment: C: multiple bed - merge regions IF overlapping more than xx percent of size
... If you are looking at 3 separate bed files representing 3 replicates for instance, how would you go about limiting the printed result with this method to only elements present in all 3 of the replicates (at some % overlap)? Thanks. ...
written 18 days ago by rbronste290
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Comment: C: Limiting interval sizes with awk
... This seems to work fine: awk '{if($3-$2 >= 150 && $3-$2 <= 200) print}' test.bedpe > test_between_150-200.bedpe ...
written 6 weeks ago by rbronste290
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Limiting interval sizes with awk
... Kind of a basic awk question. I have a bed file where I have been doing the following to limit interval sizes to those under 1000bp with the following awk script, how would I go about doing the same thing but limiting the output to those between 150-200bp only? Thanks! awk '{if($3-$2 <= 1000 ...
bedtools bed bedops awk interval written 6 weeks ago by rbronste290
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Comment: C: Bamtobed paired mate error
... Yes you are correct it is a warning however still would like to figure out a fix as its severely reducing the bedpe information I get. ...
written 7 weeks ago by rbronste290

Latest awards to rbronste

Popular Question 3 days ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 25 days ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
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Great Question 6 months ago, created a question with more than 5,000 views. For Trouble installing R package Cairo
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Popular Question 18 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?

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