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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 |
