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robertaboukhalil / ginkgo

Cloud-based single-cell copy-number variation analysis tool
qb.cshl.edu/ginkgo
BSD 2-Clause "Simplified" License
47 stars 28 forks source link

Bad Bin -> coordinate map? #24

Closed kunalkathuria closed 4 years ago

kunalkathuria commented 5 years ago

I was wondering if there is a file somewhere that would map bin numbers to genomic hg 19 coordinates (e.g. for 500 kb variable bins) so that I can know which regions are masked by the bad-bin analysis? Thank you,

Kunal

robertaboukhalil commented 4 years ago

Hi Kunal, yes, in the files you downloaded that contain the genome coordinates, there should be a file that looks something like e.g. variable_500000_101_bowtie, where the line number (excluding the header) should be the bin ID

kunalkathuria commented 4 years ago

Thank you!