Table 3 Plastid’s command-line scripts automate common analysis tasks
From: Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
Analysis of count and alignment data | |
counts_in_region | Count the number of read alignments covering arbitrary regions of interest in the genome, and calculate read densities (in reads per nucleotide and in RPKM) over these regions |
cs | Count the number of read alignments and calculate read densities (in RPKM) specifically for genes and sub-regions (5′ UTR, CDS, 3′ UTR), correcting gene and sub-region boundaries for overlapping genes |
get_count_vectors | Fetch vectors of counts at each nucleotide position in one or more regions of interest, saving each vector as its own line-delimited text file |
make_wiggle | Create wiggle or bedGraph files from alignment files after applying a read mapping rule (e.g. to map ribosome-protected footprints at their P-sites), for visualization in a genome browser |
metagene | Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest |
phase_by_size | Estimate sub-codon phasing in ribosome profiling data |
psite | Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length |
Manipulation of genomic features | |
crossmap | Empirically annotate multimapping regions of a genome, given alignment criteria |
gff_parent_types | Determine parent-child relationships of features in a GFF3 file |
reformat_transcripts | Convert transcripts between BED, BigBed, GTF2, GFF3, and PSL formats |
findjuncs | Find all unique splice junctions in one or more transcript annotations, and optionally export these in Tophat’s.juncs format |
slidejuncs | Compare a set of splice junctions to a reference set, and, if possible with equal sequence support, slide discovered junctions to compatible known junctions |