User: shubhibartaria

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Posts by shubhibartaria

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DiffBind affinity vs occupancy Heatmaps
... Hi, I wanted to know whether the first occupancy heatmap that is generated is based on the scores that the BED files contain or are the scores calculated by Diffbind itself? What if the bed files do not have a score column (only chr #, start, end, name is present)? How is the score calculated then? ...
diffbind heatmap pearsoncorrelation written 3.4 years ago by shubhibartaria0 • updated 3.4 years ago by Rory Stark2.9k
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Comment: C: Regarding general understanding of DiffBind
... I hope Rory responds with a way to incorporate exact values into the heatmap. And my BED files doesn't have a score column. It just has 4 columns ...
written 3.4 years ago by shubhibartaria0
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Answer: A: Regarding general understanding of DiffBind
... I just faced another dilemma. When I used the dba.count after adding one more bed and bam file which was a combination of all the other 3 files(Mid Brain 1,2,3), I got a plot which was a little different than the one I plotted without the Joint file. Now, if comparison was a pairwise comparison, how ...
written 3.4 years ago by shubhibartaria0
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Comment: C: Regarding general understanding of DiffBind
... And when you say score in the peak files, does that mean an explicit column in the BED files or it calculates it on its own? Does the first one only use the BED files and the second uses both BED and BAM files? ...
written 3.4 years ago by shubhibartaria0
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Answer: A: Regarding general understanding of DiffBind
... This is sessionInfo() output R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.4 (El Capitan) locale: [1] C attached base packages: [1] stats4    parallel  stats     graphics  grDevices utils     datasets  [8] methods   base      other attached ...
written 3.4 years ago by shubhibartaria0
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Regarding general understanding of DiffBind
... Hello, This question is from a rookie in terms of wet lab techniques and new student into bioinformatics. I am working in a lab in Johns Hopkins wherein I am given a few BED and BAM files to analyse and see how similar they are. I am using the diffbind package to do so. The first correlation map(he ...
diffbind heatmap written 3.4 years ago by shubhibartaria0

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