User: bernatgel
bernatgel • 1.2k
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Posts by bernatgel
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... Hi Vijay,
As Bastien said, karyoploteR does not need the reference sequence or anything like that. It just needs the chromosome lengths, which facilitates working with custom and unfinished genomes.
I would do something along the lines of what Bastien suggested.
1. Create a GRanges object with ...
written 4 days ago by
bernatgel • 1.2k
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... Just for future reference, the problem in this case was that the version of [karyoploteR](http://bioconductor.org/packages/karyoploteR/) was an old one, from before the [kpPlotLinks](https://bernatgel.github.io/karyoploter_tutorial/Tutorial/PlotLinks/PlotLinks.html) function was added. The [karyoplo ...
written 5 days ago by
bernatgel • 1.2k
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... With [karyoploteR](http://bioconductor.org/packages/karyoploteR/) you plot the peaks from the different timepoints in a single "track" creting an overlay. Depending on the format of your data you could either peak intervals with [`kpPlotRegions`](https://bernatgel.github.io/karyoploter_tutorial//Tut ...
written 8 weeks ago by
bernatgel • 1.2k
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... For an image like this you can also use karyopoteR, but use the [`kpPoints`](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Points/Points.html) function instead of `kpSegments`. You'll need to figure out the values they are plotting (the Z-score it seems) in your output files, load it in ...
written 8 weeks ago by
bernatgel • 1.2k
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... Hi nkausthu,
I cannot see the image attached. Can you fix the link? ...
written 8 weeks ago by
bernatgel • 1.2k
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... Hi @nkausthu,
I've not used XHMM myself, but if you can load the data into R, you can plot the data using [karyoploteR](http://bioconductor.org/packages/karyoploteR/).
I've created a small simulated results using the .xcnv as decribed in the [XHMM tutorial](https://atgu.mgh.harvard.edu/xhmm/tutor ...
written 8 weeks ago by
bernatgel • 1.2k
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... I like the explicit error management described [here][1], with a try, yell and die functions. As a bonus, you can modify die to do some additional logging of errors before actually dying and returning. It might be useful in addition to pipefail
yell() { echo "$0: $*" >&2; }
die() { y ...
written 11 weeks ago by
bernatgel • 1.2k
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Comment:
C: Tools for visualizing genome
... Aritra,
We would need more information to help you. Do you have the positions of the STRs or you need to compute them? As I understand your questio, you don't actually need to visualize the sequence, isn't it?
If you have the positions of the STR's in a BED file or similar, you can use [karyoplot ...
written 5 months ago by
bernatgel • 1.2k
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... Ok, I'll do that. thanks ...
written 6 months ago by
bernatgel • 1.2k
9
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... Note: This post was an answer to [another Tutoria doing the same with ggplot](https://www.biostars.org/p/269857/). Moved here as suggested by others.
I had to create whole genome plots with data on them more than than a few times, and it's not easy to get it right! So I finally decided to create a ...
written 6 months ago by
bernatgel • 1.2k
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