Output File Column Descriptions - McIntyre-Lab/TranD GitHub Wiki
Table of Contents
- 1 GTF Gene Mode - Event ER Output File
- 1 GTF Gene Mode - Event EF Output File
- 1 GTF Pairwise Mode - Event Output File
- 1 GTF Pairwise Mode - Pairwise Distance Output File
- 2 GTF Pairwise Mode - Pairwise Distance Output File
- 2 GTF Pairwise Minimum Mode - Pairwise Distance Additional Columns
1 GTF Gene Mode - Event ER Output File
| Column Name | Description |
|---|---|
| gene_id | Gene ID |
| transcript_id | Piped ("|") list of transcript IDs the exon region is present in |
| ER_id | Exon region ID (continuous region of exonic space present in either any transcript) |
| ER_chr | Chromosome exon region is located |
| ER_start | Start coordinate of exon region (0-based) |
| ER_end | End coordinate of exon region |
| ER_strand | Strand of exon region |
| exons_per_ER | Number of exons in exonic region |
| exon_id | Piped ("|") list of exon IDs that are contained within the exon region |
| transcripts_per_ER | Number of transcripts assoicated with the exon region |
| annotation_frequency | Annotation frequency as either “unique”, “common”, “constitutive” |
| flag_ER_IR | Binary indicator (1,0) if the exon region contains an intron retention event (where an intron of one transcript is entirely contained within an exon of the other transcript) |
1 GTF Gene Mode - Event EF Output File
| Column Name | Description |
|---|---|
| gene_id | Gene ID |
| transcript_id | Piped ("|") list of transcript IDs the EF is present in |
| EF_id | EF ID (distinct exon EF present in any transcript in the gene), formatted as [associated exon region ID]:[EF number within exon region] |
| EF_chr | Chromosome EF is located |
| EF_start | Start coordinate of EF (0-based) |
| EF_end | End coordinate of EF |
| EF_strand | Strand of EF |
| ER_id | Exon region ID the EF is contained within (continuous region of exonic space present in either any transcript) |
| ER_chr | Chromosome exon region is located |
| ER_start | Start coordinate of exon region (0-based) |
| ER_end | End coordinate of exon region |
| ER_strand | Strand of exon region |
| exon_id | Piped ("|") list of exon IDs that are contained within the EF |
| exons_per_EF | Number of exons in EF |
| transcripts_per_EF | Number of transcripts assoicated with the EF |
| annotation_frequency | Annotation frequency as either “unique”, “common”, “constitutive” |
| flag_EF_IR | Binary indicator (1,0) if the EF is involved in an intron retention event (where an intron of one transcript is entirely contained within an exon of the other transcript) |
1 GTF Pairwise Mode - Event Output File
| Column Name | Description |
|---|---|
| gene_id | Gene ID |
| transcript_1 | Transcript ID for transcript 1 |
| transcript_2 | Transcript ID for transcript 2 |
| transcript_id | Piped ("|") list of transcript IDs the EF is present in (if only in transcript 1 then transcript_id = transcript_1, if only in transcript 2 then transcript_id = transcript_2, if present in both then transcript_id = transcript_1|transcript_2) |
| EF_id | EF ID (distinct exon EF present in either transcript 1 or transcript 2) |
| EF_chr | Chromosome EF is located |
| EF_start | Start coordinate of EF (0-based) |
| EF_end | End coordinate of EF |
| EF_strand | Strand of EF |
| ER_id | Exon region ID the EF is contained within (continuous region of exonic space present in either transcript 1 or transcript 2) |
| ER_chr | Chromosome exon region is located |
| ER_start | Start coordinate of exon region (0-based) |
| ER_end | End coordinate of exon region |
| ER_strand | Strand of exon region |
| flag_EF_IR | Binary indicator (1,0) if the EF is involved in an intron retention event (where an intron of one transcript is entirely contained within an exon of the other transcript) |
1 GTF Pairwise Mode - Pairwise Distance Output File
| Column Name | Description |
|---|---|
| gene_id | Gene ID |
| transcript_1 | Transcript ID for transcript 1 (T1) |
| transcript_2 | Transcript ID for transcript 2 (T2) |
| num_jxn_only_T1 | Number of junctions in transcript 1 only |
| num_jxn_only_T2 | Number of junctions in transcript 2 only |
| num_jxn_same | Number of junctions same in transcript 1 and transcript 2 |
| prop_jxn_same | Proportion of shared junctions (num_jxn_same/(num_jxn_only_T1 + num_jxn_only_T2 + num_jxn_same)) |
| prop_jxn_notSame | 1 - prop_jxn_same |
| jxn_string_T1 | Piped ("|") list of all junction IDs (chr:start:end:strand) in transcript 1 |
| jxn_string_T2 | Piped ("|") list of all junction IDs (chr:start:end:strand) in transcript 2 |
| jxn_only_T1 | Piped ("|") list of junction IDs (chr:start:end:strand) in transcript 1 only |
| jxn_only_T2 | Piped ("|") list of junction IDs (chr:start:end:strand) in transcript 2 only |
| jxn_same | Piped ("|") list of junction IDs (chr:start:end:strand) same in transcript 1 and transcript 2 |
| num_ER_only_T1 | Number of exon regions in transcript 1 only |
| num_ER_only_T2 | Number of exon regions in transcript 2 only |
| num_ER_ovlp | Number of exon regions overlapping by transcript 1 and transcript 2 |
| prop_ER_ovlp | Proportion of overlapping exon regions (num_ER_ovlp/(num_ER_only_T1 + num_ER_only_T2 + num_ER_ovlp)) |
| prop_ER_noOvlp | 1 - prop_ER_ovlp |
| ER_only_T1 | Piped ("|") list of exon region IDs in transcript 1 only |
| ER_only_T2 | Piped ("|") list of exon region IDs in transcript 2 only |
| ER_ovlp | Piped ("|") list of exon region IDs overlapping by transcript 1 and transcript 2 |
| num_EF_only_T1 | Number of exon EFs in transcript 1 only |
| num_EF_only_T2 | Number of exon EFs in transcript 2 only |
| num_EF_ovlp | Number of exon EFs overlapping by transcript 1 and transcript 2 |
| prop_EF_ovlp | Proportion of overlapping exon EFs (num_EF_ovlp/(num_EF_onlyt_T1 + num_EF_only_T2 + num_EF_ovlp)) |
| prop_EF_noOvlp | 1 - prop_EF_ovlp |
| EF_only_T1 | Piped ("|") list of exon EF IDs in transcript 1 only |
| EF_only_T2 | Piped ("|") list of exon EF IDs in transcript 2 only |
| EF_ovlp | Piped ("|") list of exon EF IDs shared by transcript 1 and transcript 2 |
| num_exon_only_T1 | Number of full exons in transcript 1 only |
| num_exon_only_T2 | Number of full exons in transcript 2 only |
| num_exon_ovlp | Number of full exons overlapping by transcript 1 and transcript 2 |
| num_IR_EF_T1 | Number of intron retention events in transcript 1 (where an intron of transcript 2 is entirely contained within an exon of transcript 2) |
| num_IR_EF_T2 | Number of intron retention events in transcript 2 (where an intron of transcript 1 is entirely contained within an exon of transcript 2) |
| IR_EF_T1 | Piped ("|") list of intron IDs (chr:start:end:strand) retained in transcript 1 |
| IR_EF_T2 | Piped ("|") list of intron IDs (chr:start:end:strand) retained in transcript 2 |
| num_nt_ovlp | Number of nucleotides overlapping in transcript 1 and transcript 2 |
| num_nt_only_T1 | Number of nucleotides in transcript 1 only |
| num_nt_only_T2 | Number of nucleotides in transcript 2 only |
| num_nt_noOvlp | Number of nucleotides exclusive to transcript 1 or transcript 2 |
| total_nt | Total number of nucleotides covered by either transcript 1 or transcript 2 (union) |
| prop_nt_noOvlp | Proportion of different nucleotides ((num_nt_only_T1 + num_nt_only_T2)/total_nt) |
| prop_nt_ovlp | Proportion of shared nucleotides (num_nt_ovlp/total_nt) |
| num_nt_only_T1_in_ovlpER | Number of nucleotides in transcript 1 only in shared exon regions |
| num_nt_only_T2_in_ovlpER | Number of nucleotides in transcript 2 only in shared exon regions |
| num_nt_ovlp_in_ovlpER | Number of nucleotides shared by transcript 1 and transcript 2 in shared exon regions |
| total_nt_in_ovlpER | Total number of nucleotides in shared exon regions |
| prop_nt_noOvlp_in_ovlpER | Proportion of different nucleotides in shared exon regions ((num_nt_only_T1_ovlpER + num_nt_only_T2_ovlpER)/total_nt_in_ovlpER) |
| prop_nt_ovlp_in_ovlpER | Proportion of shared nucleotides (num_nt_ovlp_in_ovlpER/total_nt_in_ovlpER) |
| num_nt_only_T1_in_uniqER | Number of nucleotides in transcript 1 only in exon regions unique to transcript 1 |
| num_nt_only_T2_in_uniqER | Number of nucleotides in transcript 2 only in exon regions unique to transcript 2 |
| flag_FSM | Binary indicator (1,0) if transcript 1 and transcript 2 are full-splice matches (FSM) where prop_jxn_noOvlp == 0 |
| flag_T1_ISM_of_T2 | Binary indicator (1,0) if transcript 1 is an incomplete-splice match (ISM) of transcript 2, where the junctions of transcript 1 are a sequential subset of the junctions in transcript 2 |
| flag_T2_ISM_of_T1 | Binary indicator (1,0) if transcript 2 is an incomplete-splice match (ISM) of transcript 1, where the junctions of transcript 2 are a sequential subset of the junctions in transcript 1 |
| flag_IR | Binary indicator (1,0) if there is an intron retention event in the pair (num_IR_T1 + num_IR_T2 > 0) |
| flag_5_var | Binary indicator (1,0) if there is a difference in 5' transcript end positions between the pair of transcripts |
| flag_3_var | Binary indicator (1,0) if there is a difference in 3' transcript end positions between the pair of transcripts |
| flag_alt_DA | Binary indicator (1,0) if there is an alternate donor and/or alternate acceptor in the pair (num_nt_only_T1_in_ovlpER + num_nt_only_T2_in_ovlpER > 0) |
| flag_alt_exon | Binary indicator (1,0) if there is an alternate exon in the pair (unique exon region in either transcript) |
| flag_no_ovlp_nt | Binary indicator (1,0) if the transcripts do not overlap and share no nucleotides (num_ovlp_nt == 0) |
2 GTF Pairwise Mode - Pairwise Distance Output File
| Column Name | Description |
|---|---|
| gene_id | Gene ID |
| transcript_1 | Transcript ID for transcript in GTF 1 (T1) |
| transcript_2 | Transcript ID for transcript in GTF 2 (T2) |
| num_jxn_only_T1 | Number of junctions in transcript 1 only |
| num_jxn_only_T2 | Number of junctions in transcript 2 only |
| num_jxn_same | Number of junctions same in transcript 1 and transcript 2 |
| prop_jxn_same | Proportion of shared junctions (num_jxn_same/(num_jxn_only_T1 + num_jxn_only_T2 + num_jxn_same)) |
| prop_jxn_notSame | 1 - prop_jxn_same |
| jxn_string_T1 | Piped ("|") list of all junction IDs (chr:start:end:strand) in transcript 1 |
| jxn_string_T2 | Piped ("|") list of all junction IDs (chr:start:end:strand) in transcript 2 |
| jxn_only_T1 | Piped ("|") list of junction IDs (chr:start:end:strand) in transcript 1 only |
| jxn_only_T2 | Piped ("|") list of junction IDs (chr:start:end:strand) in transcript 2 only |
| jxn_same | Piped ("|") list of junction IDs (chr:start:end:strand) same in transcript 1 and transcript 2 |
| num_ER_only_T1 | Number of exon regions in transcript 1 only |
| num_ER_only_T2 | Number of exon regions in transcript 2 only |
| num_ER_ovlp | Number of exon regions overlapping by transcript 1 and transcript 2 |
| prop_ER_ovlp | Proportion of overlapping exon regions (num_ER_ovlp/(num_ER_only_T1 + num_ER_only_T2 + num_ER_ovlp)) |
| prop_ER_noOvlp | 1 - prop_ER_ovlp |
| ER_only_T1 | Piped ("|") list of exon region IDs in transcript 1 only |
| ER_only_T2 | Piped ("|") list of exon region IDs in transcript 2 only |
| ER_ovlp | Piped ("|") list of exon region IDs overlapping by transcript 1 and transcript 2 |
| num_EF_only_T1 | Number of exon EFs in transcript 1 only |
| num_EF_only_T2 | Number of exon EFs in transcript 2 only |
| num_EF_ovlp | Number of exon EFs overlapping by transcript 1 and transcript 2 |
| prop_EF_ovlp | Proportion of overlapping exon EFs (num_EF_ovlp/(num_EF_onlyt_T1 + num_EF_only_T2 + num_EF_ovlp)) |
| prop_EF_noOvlp | 1 - prop_EF_ovlp |
| EF_only_T1 | Piped ("|") list of exon EF IDs in transcript 1 only |
| EF_only_T2 | Piped ("|") list of exon EF IDs in transcript 2 only |
| EF_ovlp | Piped ("|") list of exon EF IDs shared by transcript 1 and transcript 2 |
| num_exon_only_T1 | Number of full exons in transcript 1 only |
| num_exon_only_T2 | Number of full exons in transcript 2 only |
| num_exon_ovlp | Number of full exons overlapping by transcript 1 and transcript 2 |
| num_IR_EF_T1 | Number of intron retention events in transcript 1 (where an intron of transcript 2 is entirely contained within an exon of transcript 2) |
| num_IR_EF_T2 | Number of intron retention events in transcript 2 (where an intron of transcript 1 is entirely contained within an exon of transcript 2) |
| IR_EF_T1 | Piped ("|") list of intron IDs (chr:start:end:strand) retained in transcript 1 |
| IR_EF_T2 | Piped ("|") list of intron IDs (chr:start:end:strand) retained in transcript 2 |
| num_nt_ovlp | Number of nucleotides overlapping in transcript 1 and transcript 2 |
| num_nt_only_T1 | Number of nucleotides in transcript 1 only |
| num_nt_only_T2 | Number of nucleotides in transcript 2 only |
| num_nt_noOvlp | Number of nucleotides exclusive to transcript 1 or transcript 2 |
| total_nt | Total number of nucleotides covered by either transcript 1 or transcript 2 (union) |
| prop_nt_noOvlp | Proportion of different nucleotides ((num_nt_only_T1 + num_nt_only_T2)/total_nt) |
| prop_nt_ovlp | Proportion of shared nucleotides (num_nt_ovlp/total_nt) |
| num_nt_only_T1_in_ovlpER | Number of nucleotides in transcript 1 only in shared exon regions |
| num_nt_only_T2_in_ovlpER | Number of nucleotides in transcript 2 only in shared exon regions |
| num_nt_ovlp_in_ovlpER | Number of nucleotides shared by transcript 1 and transcript 2 in shared exon regions |
| total_nt_in_ovlpER | Total number of nucleotides in shared exon regions |
| prop_nt_noOvlp_in_ovlpER | Proportion of different nucleotides in shared exon regions ((num_nt_only_T1_ovlpER + num_nt_only_T2_ovlpER)/total_nt_in_ovlpER) |
| prop_nt_ovlp_in_ovlpER | Proportion of shared nucleotides (num_nt_ovlp_in_ovlpER/total_nt_in_ovlpER) |
| num_nt_only_T1_in_uniqER | Number of nucleotides in transcript 1 only in exon regions unique to transcript 1 |
| num_nt_only_T2_in_uniqER | Number of nucleotides in transcript 2 only in exon regions unique to transcript 2 |
| flag_FSM | Binary indicator (1,0) if transcript 1 and transcript 2 are full-splice matches (FSM) where prop_jxn_noOvlp == 0 |
| flag_T1_ISM_of_T2 | Binary indicator (1,0) if transcript 1 is an incomplete-splice match (ISM) of transcript 2, where the junctions of transcript 1 are a sequential subset of the junctions in transcript 2 |
| flag_T2_ISM_of_T1 | Binary indicator (1,0) if transcript 2 is an incomplete-splice match (ISM) of transcript 1, where the junctions of transcript 2 are a sequential subset of the junctions in transcript 1 |
| flag_IR | Binary indicator (1,0) if there is an intron retention event in the pair (num_IR_T1 + num_IR_T2 > 0) |
| flag_5_var | Binary indicator (1,0) if there is a difference in 5' transcript end positions between the pair of transcripts |
| flag_3_var | Binary indicator (1,0) if there is a difference in 3' transcript end positions between the pair of transcripts |
| flag_alt_DA | Binary indicator (1,0) if there is an alternate donor and/or alternate acceptor in the pair (num_nt_only_T1_in_ovlpER + num_nt_only_T2_in_ovlpER > 0) |
| flag_alt_exon | Binary indicator (1,0) if there is an alternate exon in the pair (unique exon region in either transcript) |
| flag_no_ovlp_nt | Binary indicator (1,0) if the transcripts do not overlap and share no nucleotides (num_ovlp_nt == 0) |
2 GTF Pairwise Minimum Mode - Pairwise Distance Additional Columns
| Column Name | Description |
|---|---|
| num_transcript_inGene_{NAME1} | The number of transcripts from the first transcriptome in the given gene. NAME1 indicates the label given for the first transcriptome (default: “d1”) |
| num_transcript_inGene_{NAME2} | The number of transcripts from the second transcriptome in the given gene. NAME2 indicates the label given for the first transcriptome (default: “d2”) |
| flag_{NAME1}_greater | Binary indicator (1,0) if the first transcriptome (given label NAME1) has more transcripts that the second transcriptome within the given gene (num_transcript_inGene_{NAME1} > num_transcript_inGene_{NAME2}, num_transcript_inGene_{NAME1} > 0, num_transcript_inGene_{NAME2} > 0) |
| flag_{NAME2}_greater | Binary indicator (1,0) if the second transcriptome (given label NAME2) has more transcripts that the first transcriptome within the given gene (num_transcript_inGene_{NAME2} > num_transcript_inGene_{NAME1}, num_transcript_inGene_{NAME1} > 0, num_transcript_inGene_{NAME2} > 0) |
| flag_match | Binary indicator (1,0) if the transcriptomes have the same number of transcripts within the given gene (num_transcript_inGene_{NAME2} == num_transcript_inGene_{NAME1}, num_transcript_inGene_{NAME1} > 0, num_transcript_inGene_{NAME2} > 0) |
| transcript_inGene | Categorical variable indicating the classification of the gene based on the transcript counts: {NAME1}_greater, {NAME2}_greater, or match |
| min_match_{NAME1} | Transcript ID from second transcriptome (with added NAME2 suffix) that is the minimum pair of the given transcript in the first transcriptome (minimum pair based on prop_jxn_noOvlp, prop_ER_noOvlp, prop_nt_noOvlp, and num_nt_noOvlp) |
| flag_min_match_{NAME1} | Binary indicatory (1,0) if the given pair is the minimum pair for the transcript in the first transcriptome (min_match_{NAME1} == transcript_2) |
| min_match_{NAME2} | Transcript ID from first transcriptome (with added NAME1 suffix) that is the minimum pair of the given transcript in the second transcriptome (minimum pair based on prop_jxn_noOvlp, prop_ER_noOvlp, prop_nt_noOvlp, and num_nt_noOvlp) |
| flag_min_match_{NAME2} | Binary indicatory (1,0) if the given pair is the minimum pair for the transcript in the second transcriptome (min_match_{NAME2} == transcript_1) |
| flag_RMP | Binary indicatory (1,0) if the given pair is the minimum pair for both transcripts (meaning that they are reciprocal minimum matches) |
| num_RMP_inGene | Number of reciprocal minimum pairs present in the given gene |
| flag_{NAME1}_tie | Binary indicatory (1,0) if the transcript in first transcriptome has a tie (or more than one) minimum matches (only 1 of the ties is flagged as the minimum but both are flagged as a tie) |
| flag_{NAME2}_tie | Binary indicatory (1,0) if the transcript in second transcriptome has a tie (or more than one) minimum matches (only 1 of the ties is flagged as the minimum but both are flagged as a tie) |
| flag_{NAME1}_distance_tie | Piped ("|") list of transcript IDs from GTF2 that are minimum distance ties of transcript_1 |
| flag_{NAME2}_distance_tie | Piped ("|") list of transcript IDs from GTF1 that are minimum distance ties of transcript_2 |
| flag_identical_RMP | Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the pair has identical coordinates |
| flag_FSM_RMP | Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of full splice matches (FSM) of each other (or they have identical junctions but potentially differ by 5’ and 3’ end) |
| flag_ERS_RMP | Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) |
| flag_ERS_noIR_RMP | Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) with IR pairs excluded |
| flag_ERS_wIR_RMP | Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) ONLY IR pairs included |
| num_identical_RMP_inGene | Number of the transcript pairs in given gene that are reciprocal minimum pair AND have identical coordinates |
| num_FSM_RMP_inGene | Number of transcript pairs in given gene that are reciprocal minimum pair AND are full splice matches (FSM) of each other (or they have identical junctions but potentially differ by 5’ and 3’ end) |
| num_ERS_RMP_inGene | Number of transcript pairs in given gene that are reciprocal minimum pair AND are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) |
| num_ERS_noIR_RMP_inGene | Number of transcript pairs in given gene that are reciprocal minimum pair AND are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) with IR pairs excluded |
| num_ERS_wIR_RMP_inGene | Number of transcript pairs in given gene that are reciprocal minimum pair AND are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) ONLY IR pairs included |
| prop_identical_RMP_inGene | Proportion of reciprocal minimum pairs that have identical coordinates |
| prop_FSM_RMP_inGene | Proportion of reciprocal minimum pairs that are full splice matches (FSM) of each other (or they have identical junctions but potentially differ by 5’ and 3’ end) |
| prop_ERS_RMP_inGene | Proportion of reciprocal minimum pairs that are exon region shared (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) |
| prop_ERS_noIR_RMP_inGene | Proportion of reciprocal minimum pairs that are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) with IR pairs excluded |
| prop_ERS_wIR_RMP_inGene | Proportion of reciprocal minimum pairs that are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) ONLY IR pairs included |
| flag_no_ovlp_nt_RMP | Binary indicator (1,0) if the transcripts are reciprocal minimum pairs AND the coordinates of the transcript pair do not overlap and therefore they do have any nucleotides in common |
| flag_alt_exon_RMP | Binary indicator (1,0) if the transcripts are reciprocal minimum pairs AND there is an alternate exon in the pair (unique exon region in either transcript) |
| flag_alt_DA_RMP | Binary indicator (1,0) if the transcripts are reciprocal minimum pairs AND there is an alternate donor and/or alternate acceptor in the pair (num_nt_only_T1_in_ovlpER + num_nt_only_T2_in_ovlpER > 0) |
| flag_IR_RMP | Binary indicator (1,0) if the transcripts are reciprocal minimum pairs AND there is an intron retention event in the pair (num_IR_T1 + num_IR_T2 > 0) |
| flag_5var_RMP | Binary indicator (1,0) if the transcripts are reciprocal minimum pairs AND there is 5’ end (or TSS) variation in the pair (starts of transcripts are not the same) |
| flag_3var_RMP | Binary indicator (1,0) if the transcripts are reciprocal minimum pairs AND there is 3’ end (or TTS) variation in the pair (ends of transcripts are not the same) |
| recip_min_pair_inGene | Categorical variable indicating the sub-classification of the gene based on the number of transcript pairs that are reciprocal minimum pairs: reciprocal_pairs (if all possible 1-to-1 pairs are reciprocal minimum pairs), partial_reciprocal_pairs (if some but not all possible pairs are reciprocal minimum pairs), or no_reciprocal_pairs (if no reciprocal pairs are found) |
| flag_min_match_{NAME1}_w_tie | Binary indicatory (1,0) if the given pair is a minimum pair for the transcript in the first transcriptome when including ties (transcript_2 in flag_{NAME1}_distance_tie) |
| flag_min_match_{NAME2}_w_tie | Binary indicatory (1,0) if the given pair is a minimum pair for the transcript in the second transcriptome when including ties (transcript_1 in flag_{NAME2}_distance_tie) |
| flag_RMP_w_tie | Binary indicatory (1,0) if the given pair is the minimum pair for both transcripts (meaning that they are reciprocal minimum matches) taking into account tied minimum pairs |
| num_RMP_inGene_w_tie | Number of possible reciprocal minimum pairs present in the given gene with taking into account tied minimum pairs |
| flag_identical_RMP_w_tie | (Taking into account ties) Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the pair has identical coordinates |
| flag_FSM_RMP_w_tie | (Taking into account ties) Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of full splice matches (FSM) of each other (or they have identical junctions but potentially differ by 5’ and 3’ end) |
| flag_ERS_RMP_w_tie | (Taking into account ties) Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) |
| flag_ERS_noIR_RMP_w_tie | (Taking into account ties) Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) with IR pairs excluded |
| flag_ERS_wIR_RMP_w_tie | (Taking into account ties) Binary indicatory (1,0) if the transcript pair is a reciprocal minimum pair AND the transcripts in the pair of exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) ONLY IR pairs included |
| num_identical_RMP_inGene_w_tie | (Taking into account ties) Number of the transcript pairs in given gene that are reciprocal minimum pair AND have identical coordinates |
| num_FSM_RMP_inGene_w_tie | (Taking into account ties) Number of transcript pairs in given gene that are reciprocal minimum pair AND are full splice matches (FSM) of each other (or they have identical junctions but potentially differ by 5’ and 3’ end) |
| num_ERS_RMP_inGene_w_tie | (Taking into account ties) Number of transcript pairs in given gene that are reciprocal minimum pair AND are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) |
| num_ERS_noIR_RMP_inGene_w_tie | (Taking into account ties) Number of transcript pairs in given gene that are reciprocal minimum pair AND are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) with IR pairs excluded |
| prop_identical_RMP_inGene_w_tie | (Taking into account ties) Proportion of reciprocal minimum pairs that have identical coordinates |
| prop_FSM_RMP_inGene_w_tie | (Taking into account ties) Proportion of reciprocal minimum pairs that are full splice matches (FSM) of each other (or they have identical junctions but potentially differ by 5’ and 3’ end) |
| prop_ERS_RMP_inGene_w_tie | (Taking into account ties) Proportion of reciprocal minimum pairs that are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) |
| prop_ERS_noIR_RMP_inGene_w_tie | (Taking into account ties) Proportion of reciprocal minimum pairs that are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) with IR pairs excluded |
| num_ERS_wIR_RMP_inGene_w_tie | (Taking into account ties) Number of transcript pairs in given gene that are reciprocal minimum pair AND are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) ONLY IR pairs included |
| prop_ERS_wIR_RMP_inGene_w_tie | (Taking into account ties) Proportion of reciprocal minimum pairs that are exon region matches (ERS) of each other (or they have identical exon regions but potentially differ by alt. 5’/3’ ends and/or alt. donor/acceptors) ONLY IR pairs included |
| recip_min_pair_inGene_w_tie | (Taking into account ties) Categorical variable indicating the sub-classification of the gene based on the number of transcript pairs that are reciprocal minimum pairs: reciprocal_pairs (if all possible 1-to-1 pairs are reciprocal minimum pairs), partial_reciprocal_pairs (if some but not all possible pairs are reciprocal minimum pairs), or no_reciprocal_pairs (if no reciprocal pairs are found) |