# Command-line scripts¶

plastid includes the following command-line scripts. Click on a name below for more information:

 Analysis of sequencing or quantitative 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) get_count_vectors Fetch vectors of counts or other quantitative data 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, optionally applying a mapping rule 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 Generating or modifying genome annotations crossmap Generate a mask file annotating regions of the genome that fail to produce uniquely mapping reads under various alignment criteria, so that they may be excluded from future analyses gff_parent_types Examine 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 splice junctions discovered in data to those in an annotation of known splice junctions, and, if possible with equal sequence support, slide discovered junctions to compatible known junctions.