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trf-pirna-profiling

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Profiles non-miRNA small RNAs - tRNA-derived fragments (tRFs/tsRNAs), piRNAs, and rRNA/snoRNA-derived species - with MINTmap, unitas, SPORTS, and proTRAC. Use when annotating all small-RNA classes in a library; quantifying tRFs at locus resolution where tRNA loci are redundant (exclusive vs ambiguous); testing the piRNA ping-pong signature; deciding whether a species is a processed functional RNA or a degradation fragment; or judging whether the prep could even capture 5'-OH/cyclic-phosphate classes.

When to use

• annotating all small-RNA classes in a library
• quantifying tRFs at locus resolution
• testing the piRNA ping-pong signature
• deciding whether a species is a processed functional RNA or a degradation fragment
• judging whether the prep could capture 5'-OH/cyclic-phosphate classes
• piRNA cluster detection
• tRF + rRF-centric biology analysis

When not to use

• known miRNAs only analysis
• plant small RNAs (24-nt siRNA, phasiRNA)

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