Create BEDPE parser - Githubissues

GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

https://jbrowse.org/jb2

Apache License 2.0

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Create BEDPE parser #306

Closed cmdcolin closed 1 year ago

cmdcolin commented 5 years ago

BEDPE data is a simple format that shows interactions between two regions of the genome, and sometimes breakend data can come in this format

Small data files could be parsed in their entirety

Larger files might need a 2D index scheme (e.g. pairix).

Many applications end up with this type of data and/or a subtype of it

gene fusion
sv
hi-c

https://github.com/cancerit/BRASS/wiki/BEDPE https://support.10xgenomics.com/genome-exome/software/pipelines/latest/output/bedpe https://docs.higlass.io/data_preparation.html

cmdcolin commented 2 years ago

random note: possible gene fusion data from TCGA here, controlled access though cc @carolinebridge-oicr https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%5B%22Transcript%20Fusion%22%5D%7D%7D%5D%7D

cmdcolin commented 2 years ago

just commenting here cause gene fusion discussion with @rbuels earlier too and cause the data format for these is bedpe