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Table 2 Plastid includes configurable mapping functions that cover many uses cases in sequencing analysis

From: Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data

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