Analysis tool for tRNA Transcriptomes and Translatomes Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues

 

1. Trim tRNA reads based on known adapter sequences with cutadapt: bash tRNA-trim.sh

2. Align tRNA reads to mouse genome with bowtie2: bash tRNA-bowtie.sh

3. Filter tRNA reads based on read length: bash tRNA-length.sh

4. Extract tRNA reads mapped to mitochondria and cytosolic tRNA: bash tRNA-mc.sh

5. Permutation analysis on anticodon of the isodecoders: Rscript tRNA_permutation.R

6. Align RiboTag RNA-seq reads to mouse rRNA with bowtie2: bash RiboTag-rmrna.sh

7. Align RiboTag RNA-seq reads to mouse genome with STAR: bash RiboTag-star.sh

8. Transcriptome assembly and abundance estimation with StringTie on RiboTag reads: bash RiboTag-stringtie.sh

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