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