User: bernatgel

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bernatgel2.0k
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@bernatgel
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Posts by bernatgel

<prev • 108 results • page 1 of 11 • next >
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Answer: A: How to draw a chromosome graph with only selected genes marked in it
... Hi @aiswaryabioinfo You can use [karyoploteR](http://bioconductor.org/packages/karyoploteR) as @RamRS has suggested with this data and it can do what I think you are requesting. The first you need is to read the data and make a GRanges with the genes library(karyoploteR) #read the ge ...
written 4 days ago by bernatgel2.0k
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Answer: A: KaryotypeR for germline mutations
... Hi @ma23, You have a few problems with your code, starting by the fact that you are reading the data twice and grepping for "#CHROM" and the header line starts with "CHROM" without hash, so it won't detect it. Basically, if you have a headerless vcf and only want to create a GRanges to plot the ...
written 14 days ago by bernatgel2.0k
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Comment: C: KaryotypeR for germline mutations
... Hi @ma23 Can you show us a few lines of the VCF? and the exact code you are using? ...
written 18 days ago by bernatgel2.0k
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Comment: C: Visualisation of ChIP-seq data in r - function errors in Gviz and biomaRt
... You can also give a try to [karyoploteR](http://bioconductor.org/packages/karyoploteR/). It's also an R/Bioconductor package with a different approach to plotting data along the genome. And it can work with any genome, including "dm6". There's a [karyoploteR tutorial](https://bernatgel.github.io/ka ...
written 21 days ago by bernatgel2.0k
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Answer: A: Visualisation of ChIP-seq data in r - function errors in Gviz and biomaRt
... Your command has a typo! it should be "chromosome" and it's "chrmosome" (missing first o) so it thinks you have specified no chromosome at all. ...
written 21 days ago by bernatgel2.0k
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Answer: C: Chromosomal location mapping for miRNAs
... To produce something similar to the second figure you can use [karyoploteR](https://bernatgel.github.io/karyoploter_tutorial/). ...
written 7 weeks ago by bernatgel2.0k
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Answer: A: visualizing the Shallow whole genome sequencing on the UCSC
... Hi Sara, If you have shallow WGS you'll probably want to plot a whole genome view or at least a chromosome-wide view. You can create these plots in R with [karyoploteR](http://bioconductor.org/packages/karyoploteR/) using the `kpBAMDensity` function: library(karyoploteR) bam.file <- "pa ...
written 8 weeks ago by bernatgel2.0k
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Answer: A: Annotating varscan2 output
... We have used [annovar](http://annovar.openbioinformatics.org/) to annotate VarScan results in VCF. It works quite well and is widely used. You'll need to decide what you want to annotate and download the annovar databases from the [annovar website](http://annovar.openbioinformatics.org/en/latest/u ...
written 9 weeks ago by bernatgel2.0k
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Answer: A: How to change a allels to illumina AB?
... Hi @hektor102 I agree with Kevin on asking your colleagues why the AB notation is needed since it's less informative than the actual alleles, specially using Illumina definition of A and B. If you are referring to the A and B alleles **as defined by Illumina** for their SNP-array technology, then ...
written 9 weeks ago by bernatgel2.0k
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Answer: A: coverage plot for all chromosomes
... You can use [karyoploteR](http://bioconductor.org/packages/release/bioc/html/karyoploteR.html) as Bastien suggested, but if you can a whole genome coverage plot I think the best approach would be to perform a bit of preprocessing instead of going directly to `kpPlotCoverage`. I would recommend usi ...
written 4 months ago by bernatgel2.0k

Latest awards to bernatgel

Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
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
Scholar 8 weeks ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 8 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
Centurion 9 weeks ago, created 100 posts.
Scholar 5 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher 5 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
Scholar 5 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 5 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 6 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 6 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 6 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 7 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 7 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 7 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 8 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
Scholar 8 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 9 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents

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