Applying tsRTools to TCGA
1. tsRFinder tool
Fields description:
- tsRNA Type: the type of tsRNA molecules
- Align Score: tsRFinder can use a scoring scheme to handle different types of mismatches / indels. Details in Tutorial page
- tsRNA Length: the length of tsRNA molecules
- Source tRNA: the source tRNA of tsRNA molecules
- Fragment Position: the position of tsRNA molecules in their source tRNAs
- RPM: the RPM value of tsRNA molecules
- White list: we analysed 37 small-RNA seq data without RNA modifications from PANDORA research, and obtained the potential tsRNA molecules as White-list by tsRFinder, SPORTS, and MINTmap tools
- Sequence: the sequence of tsRNA molecules
2. tsRTarget tool
Fields description:
- tsRNAid: uniform names of the identified tsRNAs considering sequence and tRNA type (tsRNA+amino acid type+tsRNA type+unique code). For example, tsRNA-Ala-3-0055, with the sequence TCCCCGGCATCTCCACCA, was derived from position 58-75 in tRNA-Ala-CGC-1-1 and tRNA-Ala-CGC-2-1.
- Target: the target gene name
- TargetTrans: the ENST name of the target gene
- MEF: the value of performance to evaluate the RNA-RNA interaction in canonical seed pattern
- tsRNA-target Alignment:
- Seed Mode: the partten of RNA-RNA interaction, canonical or non-canonical seed targeting.
- tRNAall: the source tRNA of tsRNA molecules
- tsRNAseq: the sequence of tsRNA molecules
- tsRNAtype: the type of tsRNA molecules
- genePos: