hg38 tracks for AnnotationHub
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@mikelove
Last seen 5 hours ago
United States

I really like to use AnnotationHub in workflows and teaching material for its simplicity. One hitch when doing human functional genomics with AHub is that there aren't many tracks available for hg38:

> length(query(ah, c("hg19","BED")))
[1] 12694
> length(query(ah, c("hg38","BED")))
[1] 0


Would it be possible for the core team to perform a bulk liftover of some of these useful ENCODE tracks so they are immediately available from AHub?

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.2         BiocGenerics_0.32.0
[5] testthat_2.3.1       rmarkdown_1.18       devtools_2.2.1       usethis_1.5.1

annotationhub • 385 views
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To take the other side of the argument, isn't it a very useful skill to know how to do a liftover? It's just a couple of steps, and I would argue it's a good thing for people to learn, so incorporating in your workflows and teaching material could be a useful addition.

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I definitely see both sides.

I'm thinking in the mindset of the "let them eat cake" principle of data analysis (video of Mine Cetinkaya-Rundel below)

I'm stretching the principle a bit, but basically that it's great if first you can do things easily and quickly show the "cake", then later show complicated things like liftover.