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cole-trapnell-lab / cicero

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Gene annotation for other chromosomes? #2

Closed lzj1769 closed 5 years ago

lzj1769 commented 5 years ago

Hi,

in the tutorial, the gene annotation of chromosome 18 was provided as an example, so my question is where I can find the annotation, or how I can generate the annotation for other chromosomes?

Thanks, Zhijian

hpliner commented 5 years ago

Hi Zhijian,

The entire hg19 genome coordinates are included in the package, it is just subsetted in the tutorial: data("human.hg19.genome")

The coordinates for other genomes/builds are available from UCSC genome browser, for example, mm10 is here: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz

Hannah