############################################################################## Large-scale Analysis of Recurrent Variants in Annotations (LARVA) REGRESSION SUITE README FILE LARVA version 2.0 July 15, 2015 Lucas Lochovsky and Jing Zhang Gerstein Lab Yale University ############################################################################## This folder contains files for doing test runs of LARVA. These files are used by the "larva-regression-suite.sh" script to evaluate that LARVA produces the correct behavior given various inputs. These input files are drawn from the "input" folder. The output is put into "actual-output" folder, and compared to the files in "expected-output" folder to verify LARVA's correctness. Assumes that the LARVA code folder is in the same folder as this regression-suite folder. Test files include: - DRM.bed: Distal regulatory module (DRM) enhancers, which regulate the expression of genes at non-adjacent sites. Source: PMID 22950945 - empty-file.txt: Self-explanatory, used for testing program behavior given erroneous input - example-annotations.txt: A set of 10 simulated annotations - example-variants-1.txt: A set of ~6 million simulated variants - example-variants-2.txt: A set of 1000 simulated variants - example-variants-3.txt: A set of 11 simulated variants - gencode.v16.promoter.bed: Promoter annotations derived from GENCODE v16. Source: gencodegenes.org - gencode.v16.utr.bed: UTR annotations derived from GENCODE v16. Source: gencodegenes.org - ultra-conserved.bed: Sites that are highly conserved across many phylogenetic branches. Source: PMID 15131266 - ultra-conserved-w-zero-len.bed: Malformed ultra-conserved annotation file, used for testing program behavior given erroneous input - ultra-sensitive.bed: Noncoding regions under higher selective pressure than most other noncoding regions. Source: PMID 24092746