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Where is os.environ['GENOMEDIR'] = 'genomes/Homo_sapiens/UCSC/hg19' sourced from? #9

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cgpu opened this issue Nov 17, 2019 · 0 comments

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@cgpu
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cgpu commented Nov 17, 2019

Hi,

I am trying to run the Zika.ipynb.

GENOMEDIR is defined,

os.environ['GENOMEDIR'] = 'genomes/Homo_sapiens/UCSC/hg19')

image

What files is the minimal set of reference files (eg, fasta, fai, dict) which should be included in the directory? I would like to use the reference resource for UCSC/hg19 from iGenomes but not sure how many and which files are required.

Apologies if this is described in the docs and I have missed it.

Thanks in advance,
Christina

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