User: bernatgel
bernatgel • 1.5k
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- @bernatgel
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- b********@gmail.com
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Posts by bernatgel
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4
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288
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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
bernatgel • 1.5k
1
vote
1
answer
88
views
1
answers
... 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
bernatgel • 1.5k
1
vote
2
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122
views
2
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... Yes, that's the one you need ...
written 28 days ago by
bernatgel • 1.5k
1
vote
2
answers
122
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2
answers
... 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
bernatgel • 1.5k
1
vote
1
answer
207
views
1
answers
... 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
bernatgel • 1.5k
1
vote
1
answer
207
views
1
answers
... 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
bernatgel • 1.5k
3
votes
1
answer
207
views
1
answers
... 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
bernatgel • 1.5k
1
vote
1
answer
206
views
1
answers
... 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
bernatgel • 1.5k
1
vote
2
answers
150
views
2
answers
... 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
bernatgel • 1.5k
1
vote
5
answers
167
views
5
answers
... 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
bernatgel • 1.5k
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