Translation_Error_Analysis_in_Drosophila

# Translation Error Analysis in Drosophila

## I. Introduction

**The purpose of this script is to detect translation error events and identify the characters of error events. Please refer to our article for specific experimental design and description.**

## II. Indication of script functions:

**01: Detection of translation error, calculation of translation error rate and analyzing peptide intensities.**

**02: Characterizing translation error.**

**03: Addressing bias and the influence of mass spectrometry throughput on error detection.**

**04: Reducing bias through down-sampling.**

**05: Reducing bias through linear mixed model.**

**06: Ribo-seq coverage analysis.**

**07: Detecting positive selection on codon optimization.**

**Sup_01, Sup_06: Simulating multiple-hits under Poisson distribution.**

**Sup_02: Gene ontology analysis of genes detected with translation error.**

**Sup_03: Correlation of number of substitutions and developmental stages.**

**Sup_04: Calculation of RSCU value and categorization of codon types.**

**Sup_05: Percentage of optimal codons in conservative/nonconservative sites.** 

**bcf_call.sh: Detecting rare SNPs using BCFtools.**

## III. Indication of figures in scripts:

**01: Figure 1b, 2c, 2d, 2e. Supplementary Figure S2, S4.**

**02: Figure 1e, 1f.**

**03: Figure 2a, 2b, 2f.**

**04: Figure 3a.**

**05: Figure 3b, 3c, 3d. Supplementary Figure S18, S19.**

**06: Figure 4. Supplementary Figure S10-S14, S21.**

**07: Figure 5. Supplementary Figure S15.**

**Sup_01: Supplementary Figure S3.**

**Sup_02: Supplementary Figure S5.**

**Sup_03: Supplementary Figure S6-S8.**

**Sup_05: Supplementary Figure S17, S20.**

## IV. License

**Each file included in this repository is licensed under the MIT License.**