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yihchii / hippie

HIPPIE - a high-throughput identification pipeline for promoter interacting enhancer elements
http://wanglab.pcbi.upenn.edu/hippie
MIT License
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annotation #1

Closed fcgportal closed 8 years ago

fcgportal commented 9 years ago

Dear ‘hippie’ developers, Thanks for developing ‘hippie’! It is of a great interest for us to be able to discover enhancer–target gene interactions using Hi-C. Since our in-house data is based on current Gencode Annotation (Ensembl v79), just wondering is there an instruction to produce "hippie_annot_hg38/database" using Ensembl v79 ? We would be very appreciable if you could advise us what could be amend in our procedure. Thank you again.

yihhwang commented 9 years ago

Hi @dreamingest ,

Thanks you for your message. Please refer to our parsed annotation data at: hippie website. In the hippie_annot_hg19.tar.gz package, you could find database/download_read.txt and database/README_BED.sh as the scripts for generating the hippie_annot_hg19/database/ folder. Please amend hg19 toward hg38 from the two scripts, in order to work on the latest (hg38) assembly.

fcgportal commented 9 years ago

Hi Yihchii, Thank you so much for your kind help. I've already produced a "hippie_annot_hg38/database". It seemed good! One more thing, do you have any suggestion on making "hippie_annot_hg38/chromosomes" other than just liftover it from hg19 to hg38? Thank you again.

yihhwang commented 9 years ago

Hi @dreamingest , We suggest you to do liftover from hg19 to hg38 for the chromosomes / folder. The actual calculation of mappability and gc content requires not only parsing but also re-mapping on the simulated data, and liftover is a relatively efficient way for getting the reliable coordinates with their values.