bookend-rna 0.0.5

End-guided transcript assembler for short and long RNA-seq reads.

/| 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.