CHyMErA_exonDelScoring

Code to score CHyMErA exon deletions

Using read counts per guide pair as well as dropout scores from https://github.com/HenryWard/chymera-scoring, together with auxiliary information about exons such as expression and splicing status in the screened cell type, exons are scored for growth phenotypes based on the proportion of exon-deletion (intronic-intronic) guide pairs that drop out significantly.

Input

Screen data

• exon_deletion_norm_counts.txt.gz: Raw read counts and log2-fold changes per guide pair
• intronic_intronic_guides.tsv.gz: Mean log2-fold change and empirical FDR per intronic-intronic guide pair. See here for derivation.
• other_guides.tsv.gz: Same as above, for other types of guide pairs

Exon annotation

• Knockout.exons.human.csv.gz: Exon annotation from screen design phase

Additional information about gene expression and splicing in cell type

This was obtained using vast-tools on RNA-Seq data from RPE1 cells, GEO: GSE75189

• cRPKM_AND_COUNTS-Hsa1.tab.gz Gene expression in RPE1
• INCLUSION_LEVELS_FULL-Hsa1-hg19.tab.gz Alternative splicing percent-spliced-in in RPE1

Output

• Fitness.RPE1.pdf: Fitness effect (drop-out) of exonic Cas9 guides and annotation of essentiality cutoffs
• Essentiality_RNAseq.pdf: Mean fFitness effect of exonic Cas9 guides vs. expression of host genes and PSI of targeted alternative exons, showing that only expressed genes have fitness effects in the screen.
• Knockout.exons_RPE1.pdf: Numbers of exons by type according to an annotation modified by expression and splicing data from the same cell line.
• ExonDeletionScores.RPE1.csv: Table of signifcantly dropping out exon-targeting and control guide pairs, and hit annotation (Fig. 6a, left)
• ScreenPerformance.RPE1.exonDelPairs.pdf: Hit calling at various thresholds for proportion of guides that exhibit drop-out, for intronic-intronic guide pairs. (Fig. 6a, right)
• ScreenPerformance.cutoffs.RPE1.singleCutPairs.pdf: Hit calling at various thresholds for proportion of guides that exhibit drop-out, for intronic-intergenic control guide pairs.
• HitCalling_0.18.pdf: Rate of hits called at selected threshold of 18% of intronic-intronic guide pairs per exon (Fig. 6b)
• Hits_RPE1_0.18.properties.pdf: Fitness effect of exonic Cas9 guides for genes with significant exons (Fig. 6d) and exon legnth of significant and non-significant exons (Fig. S6a)