Table 2.

Plastid includes configurable mapping functions that cover many uses cases in sequencing analysis

Method	Map reads	Sample use
Fiveprime	At a fixed offset from their 5′ ends	Ribosome profiling with RNase I (e.g. yeast, human), RNA-seq
Threeprime	At a fixed offset from their 3′ ends	Ribosome profiling with RNase I, RNA-seq
Fiveprime, variable	At an offset from 5′ end determined by read length	Ribosome profiling with RNase I, RNA-seq
Fiveprime, variable and stratified by read length	At an offset from 5′ end determined by read length, partitioning reads of each length into separate arrays	ORF annotation from ribosome profiling data
Center-weighted	Fractionally over entire length, optionally trimming a fixed number of nucleotides from the 5′ and 3′ ends	Ribosome profiling with MNase (e.g. E. coli & D. melanogaster), RNA-seq