Command-line scripts¶
plastid
includes the following command-line scripts. Click on a name below for more information:
Analysis of sequencing or quantitative data
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
Count the number of read alignments and calculate read densities (in RPKM) specifically for genes and sub-regions (5’ UTR, CDS, 3’ UTR)
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
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
Compute a metagene profile of read alignments, counts, or quantitative data over one or more regions of interest, optionally applying a mapping rule
Estimate sub-codon phasing in ribosome profiling data
Estimate position of ribosomal P-site within ribosome profiling read alignments as a function of read length
Generating or modifying genome annotations
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
Examine parent-child relationships of features in a GFF3 file
Convert transcripts between BED, BigBed, GTF2, GFF3, and PSL formats
Find all unique splice junctions in one or more transcript annotations, and optionally export these in Tophat’s
.juncs
formatCompare 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.