User: bernatgel

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bernatgel220
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Barcelona, Spain
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@bernatgel
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Posts by bernatgel

<prev • 21 results • page 1 of 3 • next >
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Answer: A: SNP Array data with 0 copies for a segment
... If there's no normal contamination you should see a deep drop in LRR and a kind of a smear in BAF. BAF is computed as the part of the total signal that comes from the B allele. Since with an homozygous loss both alleles should have a signal 0, all signal you see will be background random noise. T ...
written 5 weeks ago by bernatgel220
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Comment: C: How to plot density between 2 bed files?
... I agree with Alex Reynolds that the small differences might come from reads counted multiple times. In the example code I've provided the windows are not overlapping but there's no check preventing a read to be counted twice in a similar way to bedops. In any case, if you need to ensure that every r ...
written 6 weeks ago by bernatgel220
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Comment: C: How to plot density between 2 bed files?
... Sure, you can specify a different genome when creating the karyoplot with `plotKaryotype(genome="hg38")` or `plotKaryotype(genome="mm10")`, for example. It has a small cache with a few frequently used organisms ans it the cache misses, it will use the available BSGenomes installed and download the c ...
written 6 weeks ago by bernatgel220
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Comment: C: How to plot density between 2 bed files?
... As far as I can see in GSM there are 4117 regions between positions 58819693 and 59363443 and in STEM there are 6958 regions between 58819362 and 59363565, so these peaks are real. I think the difference with your plots is due to the differences between GRCh37 and GRCh38. ChrY is shorter in GRCh38 ...
written 6 weeks ago by bernatgel220
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Answer: A: How to plot density between 2 bed files?
... If you prefer a pure R solution, you can user karyoploteR. The package is still in Bioconductor devel, so you will need R-devel to use it until mid April. You can compute the density and create the plot in a few lines: library(karyoploteR) window.size <- 1e5 #read the data with re ...
written 6 weeks ago by bernatgel220
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Comment: C: bedtools shuffle vs. random
... Yes, I forgot to add this to my answer. Strand specific randomization is in the pipeline but not ready yet. It is possible to do it in a strand specific way right now by defining a custom randomization function that internally randomizes separately according to strand. If you think you strand speci ...
written 6 weeks ago by bernatgel220
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Answer: A: bedtools shuffle vs. random
... If you can use R, you could user [regioneR][1] to test if there is a significant overlap between your dataset and the one from the publication. It will perform the whole process explained by @fridaymeetssunday: randomization a number of times (1000), computing the overlaps, the mean and standard dev ...
written 6 weeks ago by bernatgel220
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Answer: A: Testing for over-representation of chip-peaks
... You can use the R/Bioconductor package [regioneR][1] for this. It implements a statistical test for the association of genomic regions (such as chip peaks and exons) based on random permutations. In this case I think the best aproach would be to "flip" the question and ask whether alternatively spl ...
written 7 weeks ago by bernatgel220
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Answer: A: Plotting and Visualizing large number of genes into chromsome
... In R you can use the Bioconductor package [karyoploteR][1] (at the moment only in Bioconductor devel) to create the ideogram and plot the genes. You can plot all genes individually (either as regions or a points) or compute the gene density over the genome using a non-overlapping sliding window, for ...
written 12 weeks ago by bernatgel220
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Answer: A: Genes positioning on chromosomes
... If you have the list of genes and their positions you can use the R package [karyoploteR][1] to create the plot (still in Bioconductor devel only, though). It can create karyoplots for various organisms including Rice. In this case you'll need to have the rice [BSGenome][2] package installed. Unfort ...
written 12 weeks ago by bernatgel220

Latest awards to bernatgel

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 7 weeks ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Supporter 10 months ago, voted at least 25 times.
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 21 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Appreciated 21 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Association between bed files - statistical significance

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