NAME

tmerge

SYNOPSIS

Merge transcriptome read-to-genome alignments into non-redundant transcript models.

tmerge compares transcript structures (or read-to-genome alignments) present in the input and attempts to reduce transcript redundancy, i.e., merge compatible input transcripts into non-redundant transcript models. The program treats spliced and monoexonic reads separately (i.e., those are never merged together).

tmerge is fast and can typically process several millions of aligned long reads in a few minutes.

See DESCRIPTION below for more details.

Usage example:

tmerge --tmPrefix <custom transcript_id prefix string for output GTF> <input GTF file> > <output file>

INPUT

GTF file of read-to-genome alignments, sorted by chromosome and start position.

Only exon records are considered. Read alignments need to be uniquely identified with the transcript_id GTF attribute. transcript_id is the only mandatory GTF attribute in input records.

OPTIONS

• tmPrefix (string) = Prefix string for transcript_id identifiers in the output

  Default: '' (empty string)

  By default, output transcript_ids consist in arbitrary "TM_XXXXXXXXXXXX" strings. If tmPrefix is set, its value will prefix all transcript_id strings in the GTF output.

• minReadSupport (integer) = minimum number of times a read alignment (as defined by its exon/intron structure) needs to be present in the input. In other words, when building a transcript model, only the reads fulfilling the following conditions are considered:

  For spliced transcripts, at least minReadSupport input reads must share a given intron chain and 5' + 3' ends (+/- endFuzz bases, see below).

  For mono-exonic transcripts, at least minReadSupport input reads must share their 5' + 3' ends (+/- endFuzz bases, see below). In other words, when endFuzz = 0 (the default), only monoexonic reads with identical genome coordinates are merged.

  Default: 1

• endFuzz (positive integer) = Tolerated fuzziness of 5' and 3' ends for two reads to be considered equivalent when calculating read support (see minReadSupport option above)

  Default: 0 (i.e., no fuzziness allowed)

• exonOverhangTolerance (positive integer) = maximum number of nucleotides of terminal exon overhang allowed within an intron of another transcript during the merging of input reads. See explanation in "DESCRIPTION" below.

  Default: 0 (i.e., no exon overhang allowed)

OUTPUT

tmerge outputs non-redundant transcript models (TMs) in GTF format. Each TM entry is uniquely identified by its (arbitrary) transcript_id attribute.

The gene_id attribute has the same value as transcript_id by convention; it is therefore meaningless.

The following extra GTF attributes are present in the 9th field, in order:

• contains (string): comma-separated list of input reads (transcript_ids) contained in the TM, sorted by descending genomic size.

• contains_count (integer): number of input reads contained in the TM.

• 3p_dists_to_3p (string): comma-separated list of the distances (always positive, in bases on mature RNA, i.e. ignoring introns) of the TM's 3' end to each of the input reads 3' ends it contains. The list's order follows that of contains.

• 5p_dists_to_5p (string): comma-separated list of the distances (always positive, in bases on mature RNA, i.e. ignoring introns) of the TM's 5' end to each of the input reads 5' ends it contains. The list's order follows that of contains.

• flrpm (float): TM's expression quantification in "Full-Length Reads per Million". This corresponds to longest_FL_supporters_count divided by the number of reads (i.e., transcript_id's) present in the input.

• longest (string): comma-separated list of the longest read(s) (transcript_ids) contained in the TM. This list contains more that one item only in case of length ties. Note that the reads reported do not necessarily cover the entire length of the resulting TM.

• longest_FL_supporters (string): comma-separated list of input reads that support longest over longest's full-length (+/- endFuzz).

• longest_FL_supporters_count (integer): number of input reads that support longest over longest's full-length (+/- endFuzz).

• mature_RNA_length (integer): the mature RNA length of the TM (i.e., the sum of the lengths of all its exons)

• meta_3p_dists_to_5p (string): comma-separated list of the distances (comprised between 0 and 1, on mature RNA, i.e. ignoring introns) of the TM's 5' end to each of the input reads 3' ends it contains, normalized over the TM's mature RNA length. The list's order follows that of contains.

• meta_5p_dists_to_5p (string): comma-separated list of the distances (comprised between 0 and 1, on mature RNA, i.e. ignoring introns) of the TM's 5' end to each of the input reads 5' ends it contains, normalized over the TM's mature RNA length. The list's order follows that of contains.

• rpm (float): TM's expression quantification in "Reads per Million". This corresponds to contains_count divided by the number of reads (i.e, transcript_id's) present in the input.

• spliced (boolean): specifies if the TM is spliced (1) or monoexonic (0).

DESCRIPTION

tmerge reduces redundancy in a set of transcriptome read-to-genome alignments. It does so by looking for reads with compatible aligned structures in the input, and merging those into Transcript Models (TMs).

Pairwise compatibility between aligned structures is evaluated using the following rules:

• If both structures are spliced, they are deemed compatible if:

  • 1. at least one of their exons overlap on the same genomic strand,

  • 2. either their intron chains are equal, or one is an exact subset of the other,

    and

  • 3. there is no overlap between an exon of one structure and an intron of the other.

  Condition (2) means that tmerge will never artificially extend intron chains:

  

• If both structures are monoexonic, they are considered compatible if they overlap by at least 1 nucleotide on the same genomic strand.

• If one structure is spliced and the other monoexonic, they are not merged.

All pairs of compatible structures are then merged recursively into the longest possible TM.

exonOverhangTolerance option and splice sites

Setting this option to a positive integer can correct mismapped splice junctions that sometimes occur when aligning very short, error-rich terminal read exons:

The setting works as explained below:

AUTHOR

Julien Lagarde, CRG, Barcelona, contact julienlag@gmail.com