mim-tRNAseq

Original paper: Behrens et al., 2021, Molecular Cell 81, 1–14

Protocols paper : Behrens and Nedialkova, 2022, Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq. STAR Protocols. 3, 101579

Author:

Drew Behrens

Version:

1.2

Modification-induced misincorporation tRNA sequencing.

This package is a semi-automated analysis pipeline for the quantification and analysis of tRNA expression. Given trimmed sequencing reads in fastq format, this pipeline will:

• Cluster tRNAs, index modifications, and perform SNP-tolerant read alignment with GSNAP.

• Calculate coverage information and plots (useful for QC).

• Quantify expression.

• Calculate tRNA differential expression with DESeq2.

• Analyze functional tRNA pools and tRNA completeness via 3’-CCA analysis.

• Comprehensive modification quantification and misincorporation signature analysis.

• Detect coordination between pairs of modifications and modification-aminoacylation with SLAC (SingLe-read Analysis of Crosstalks).

Index

• mim-tRNAseq introduction
  • Method strategy
  • Deconvolution
  • SingLe-read Analysis of Crosstalks
• Quick-start guide
  • Installation
  • Dependencies
  • Usage
  • Input files
  • Pre-built references
• Outputs
• Contact
  • Authors
  • Contribute
  • Cite

Indices and tables

• Index

• Module Index

• Search Page