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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

bounds_variable files #26

Closed kunalkathuria closed 4 years ago

kunalkathuria commented 5 years ago

Hi Robert,

I am trying to run Ginkgo with a list of bad bins generated outside of Ginkgo. I was trying to understand the nature of the chromosome bounds listed in the two different boundsvariable{binSize}etc. files. Could you help? Thank you!

--Kunal

robertaboukhalil commented 4 years ago

The files bounds_variable_<binsize>_<readlength>_<aligner> contain 2 columns: the chromosome number, and the global bin number corresponding to the last bin for that chromosome.

e.g. bounds_variable_1000000_150_bwa: chr3 650 means the last bin of chromosome 3 is the 650th line in the variable_1000000_150_bwa file.

kunalkathuria commented 4 years ago

Thank you!