User: bernatgel

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bernatgel1.5k
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@bernatgel
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Posts by bernatgel

<prev • 87 results • page 1 of 9 • next >
4
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Answer: A: Visualize multiple GFF files
... Hi, If you can use R you should be able to create these plots with [karyoploteR]( http://bioconductor.org/packages/karyoploteR/). You would need to load the data into R (probably using [rtracklayer](http://bioconductor.org/packages/rtracklayer/)'s ' import' function) and then plot them using `kpPlo ...
written 8 days ago by bernatgel1.5k
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Answer: A: How to find true mutations in tumor by removing the background from matched samp
... What you want is to call **somatic variants** and for that you should use a somatic variant caller, since the problem is actually quite more complex than removing the variants present in the blood sample. There are many tools for that, for example: - [GATK Mutect2](https://software.broadinstitut ...
written 27 days ago by bernatgel1.5k
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Comment: C: Assembly conversion of large BED files
... Yes, that's the one you need ...
written 28 days ago by bernatgel1.5k
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Answer: C: Assembly conversion of large BED files
... You can use liftOver in your computer with no restrictions. We have used both the [UCSC liftOver executable](https://genome-store.ucsc.edu/) and the R [Bioconductor liftOver function](https://bioconductor.org/packages/release/workflows/html/liftOver.html) in the rtracklayer package and both have w ...
written 28 days ago by bernatgel1.5k
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Comment: C: Extracting Flanking Regions across TSS using R scripts
... Yes, to merge the regions or to manage the overlaps in any other way you don't need the sequences, you can do it with the coordinates only. ...
written 6 weeks ago by bernatgel1.5k
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Comment: C: Extracting Flanking Regions across TSS using R scripts
... An easy way to build GRanges is uding the `toGRanges` function from the package [regioneR](http://bioconductor.org/packages/regioneR/). It will read most "bed-like" formats (files, data.frames...) and transform them into GRanges objects. library(biomaRt) library(regioneR) library(BSgen ...
written 6 weeks ago by bernatgel1.5k
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Answer: A: Extracting Flanking Regions across TSS using R scripts
... You can use the appropiate BSGenome from Bioconductor (probably [BSgenome.Hsapiens.UCSC.hg19](http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/) or [BSgenome.Hsapiens.UCSC.hg38](http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/). You should: 1. Transform your list of list ...
written 6 weeks ago by bernatgel1.5k
1
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Answer: A: Plot local ancestry on chromosome
... Hi, To create an image similar to the one in the link, you can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/). You'll need the position of each of the SNPs, in addition to your values. There is a complete tutorial on creating plots at the [karyoploteR tutorial](https://bernatgel. ...
written 6 weeks ago by bernatgel1.5k
1
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150
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Answer: C: How do I subset a GRanges on chromosome, region and strand?
... If you want to use a simple selector like the one you propose, you should flip the tests for start and end: gr[seqnames(gr) == "chr2" & start(gr) < 300 & end(gr) > 200 & strand(gr) == "-"] and that should work. Using `subsetByOverlaps` could be more readable and is your bes ...
written 7 weeks ago by bernatgel1.5k
1
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Answer: A: Pulling out interval adjoining regions
... If you are using R, you can do it with the `flank` function in GenomicRanges. It takes into account the chromosome lengths, if present. https://bioconductor.org/packages/3.7/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf ...
written 7 weeks ago by bernatgel1.5k

Latest awards to bernatgel

Scholar 8 days ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 27 days ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 5 weeks ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 5 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: Testing for over-representation of chip-peaks
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
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 3 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Teacher 10 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
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Teacher 13 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 14 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 14 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
Librarian 16 months ago, created a post with more than 10 bookmarks. For karyoploteR: uncircle your genomes
Scholar 18 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
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Teacher 18 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
Appreciated 19 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents

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