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output_format.md

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TENNIS outputs

TENNIS outputs two files: output_prefix.stats and output_prefix.pred.gtf.

stats file

The file output_prefix.stats consists of several summary statistics:

  • Processed transcript groups: Total number of transcript groups analyzed. This number includes all multi-exon transcript groups but excludes all single-exon transcripts.

  • Single isoform group: Number of groups containing only one isoform. Only multi-exon isoforms are counted.

  • Excl. group w. x+ isoforms: Number of groups excluded due to extra large size, i.e. having over x+ isoforms. This parameter is set by -x or --exclude_group_size.

  • T0 groups: Number of groups that satisfy the model without additional isoforms

  • T1, T2, ..., Tm groups: Groups requiring 1, 2, ..., m novel isoforms to satisfy the model. For example, T2 groups require 2 novel isoforms to meet the model requirements. m is set by -m or --max_novel_isoform.

  • T@ groups: Groups that require at least m+1 isoforms to satisfy the model; or groups that cannot be computed within the time limit set by --time_out.

pred.gtf file

The output_prefix.pred.gtf file has a standard pdf format with additional information in the attribute column (9th column). The attributes are:

Tag Value
gene_id original gene id (same as input gtf)
transcript_id transcript id
novel_transcript_num Number of novel isoforms required by the transcript group to satisfy the evolution model. This attr reflects the T1, T2, ..., Tm information.
solutions_in This isoform is in those solutions. For example [1,2,3] means this isoform appears in solution 1, solution2, and solution 3
solutions_total_num Number of optimal solutions computed. Note this entry is different from "novel_transcript_num"
solution_unique Is the solution unique or not. Namely, solutions_total_num == 1?
mandatory This isoform appears in all solutions or not. Namely, len(solutions_in) == solutions_total_num?
PctIn Ratio of solutions that this isoform appears in. Namely, len(solutions_in) / solutions_total_num. Apparently, PctIn = 1 iff mandatory
timed_out If True, solver did not complete within the given time limit

An example of attr col:

gene_id "Dmel_CG3151"; transcript_id "Dmel_CG3151.s2959520_t2963225.novel.4"; novel_transcript_num "2"; solutions_in "[3, 4, 5]"; solutions_total_num "6"; solution_unique "False"; mandatory "False"; PctIn "0.5"; timed_out "False";