3 Quick Start

We provide example files, stored in test, to help users quickly run genetribe.

3.1 Core Workflow Using .fasta, .bed, and .chrlist

cd test/
../genetribe core -l aet -f rice
2020-05-04 21:22:52 ...prepare files...
2020-05-04 21:39:19 ...calculate BSR, CBS and Penalty...
2020-05-04 21:40:07 ...evaluate optimal α for weighting score...
2020-05-04 21:41:05 ...α = 90...
2020-05-04 21:41:05 ...merge raw score...
2020-05-04 21:41:07 ...process all chromosome pairs...
2020-05-04 21:41:07 ...number of rounds: 1 ...
2020-05-04 21:41:11 ...merged results...
2020-05-04 21:41:12 ...done!

genetribe will save the output files in the current working directory

ls
aet_rice.one2many   rice_aet.one2many     aet_rice.one2one
rice_aet.one2one    aet_rice.RBH          aet_rice.SBH
rice_aet.SBH        aet_rice.singleton    rice_aet.singleton
aet_rice.block_pos  rice_aet.block_pos

3.2 Homology Inference for Same Assembly Using .bed and .genelength

cd test/
../genetribe sameassembly -l IWGSCv1p1 -f IWGSCv1
2020-05-04 21:45:42 ...prepare files...
2020-05-04 21:45:42 ...obtain overlap between genes...
2020-05-04 21:45:42 ...calculate score...
2020-05-04 21:45:42 ...generate RBH and SBH tables...
2020-05-04 21:45:43 ...done!

genetribe will save the output files in the current working directory

ls
IWGSCv1_IWGSCv1p1.one2many  IWGSCv1_IWGSCv1p1.one2one
IWGSCv1p1_IWGSCv1.one2many  IWGSCv1p1_IWGSCv1.one2one