Metadata-Version: 2.1
Name: bookend_rna
Version: 0.1.0
Summary: End-guided transcript assembler for short and long RNA-seq reads.
Home-page: https://github.com/Gregor-Mendel-Institute/bookend
Author: Michael A. Schon
Author-email: michael.schon@gmi.oeaw.ac.at
License: UNKNOWN
Description: # /| bookend |\\  
        ### End-guided transcriptome assembly.
        
        usage: bookend [subcommand] [options] [input file(s)]
        Subcommands (use -h/--help for more info):
        
            label    (Label 5' and 3' ends in a FASTQ file)
            assemble (Assemble transcripts from aligned end-labeled reads)
            merge    (Merge assembled GTFs with a reference annotation)
        
            --end-labeled read (ELR) operations--
            make-elr
            sort-elr
            combine-elr
        
            --file conversion--
            bed-to-elr
            elr-to-bed
            gtf-to-bed
            sam-to-sj
            sj-to-bed
            sj-merge
        
            --setup/indexing--
            index-fasta
            softbridge-fasta
          
            
        Converts file to a 'end labeled read' (ELR) format.
        ELR contains a two-component header: #C (chromosome) and #S (source).
        Each line is a read or read stack with six columns:
            chromosome  position  strand  ELCIGAR  sample  weight
        
            chromosome: Chromosome number, as indexed by the #C header
            position: 0-indexed position in chromosome
            strand: Inferred RNA strand; +, -, or . (unknown)
            ELCIGAR: String describing the mapped read (full description below)
            sample: Sample number, as indexed by the #S header
            weight: Read count (allows partial counts for multimappers)
          
          
        ELCIGAR strings are Character|Number strings and one trailing character
        ([CN]xC), where C is a label and N is a numeric length on the genome.
        Each C labels an end or gap in the alignment as one of the following:
            S: start
            s: start (low confidence)
            C: start (capped)
            E: end (polyA tail)
            e: end (low confidence)
            D: splice junction donor
            A: splice junction acceptor
            .: unspecified gap or end
        
        For example, a 50bp paired-end read of a 185-nt fragment would be
            .50.85.50.
        A full 3-exon transcript could be described as:
            S256D800A128D800A512E
        where the 3 exons are 256, 128, and 512 nucleotides,
        and the 2 introns are both 800 nucleotides.
Keywords: transcriptome assembler bioinformatics rna sequencing
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
