How twlab/teprof2paper works
TEProF2 is a short-read RNA-seq analysis pipeline for finding transposable-element–gene fusion transcripts, assessing their treatment enrichment, and optionally predicting transcript-derived antigens. The documented workflow annotates assembled GTFs, estimates expression, aggregates samples, evaluates supporting reads, filters candidates, merges and re-annotates transcripts, then quantifies and summarizes expression. A reference-guided route reuses prior annotations or a custom transcript set. Translation is an additional downstream capability. The README documents these stages, but the available source excerpts do not show the runtime wiring between most scripts.
Main entry points: rmskhg38_annotate_gtf_update_test_tpm.py TE fusion annotator · mergeAnnotationProcess.R Annotation merging · stringtieExpressionFrac.py Transcript expression fractions · commandsmax_speed.py Read command generation
Components 21
Fusion annotation
- Reference annotations
bin/genecode_to_dic.py - Intron annotations
bin/genecode_introns.py - TE fusion annotator
bin/rmskhg38_annotate_gtf_update_test_tpm.py - Cufflinks annotator
bin/rmskhg38_annotate_gtf_update_test_tpm_cuff.py - Reference-guided inputs
bin/mergeAnnotationProcess_Ref.R - Annotation merging
bin/mergeAnnotationProcess.R
Read evidence
- Read command generation
bin/commandsmax_speed.py - Paired-read counting
bin/rmsk_annotate_bedpe_speed.py - Single-read command generation
bin/commandsmax_speed_se.py - Single-read counting
bin/rmsk_annotate_bedse_speed.py - Candidate filtering
bin/filterReadCandidates.R
Expression analysis
- Transcript expression fractions
bin/stringtieExpressionFrac.py - Annotation statistics
bin/annotationtpmprocess.py - Sample aggregation
bin/aggregateProcessedAnnotation.R - Quantification summary
bin/finalStatisticsOutput.R
Translation
- Kozak translation
bin/translationPart1.R - Translation completion
bin/translationPart2.R
Other components
- Analyst
- Assembled GTFs
- samtools
- StringTie
Connections 24
- Analyst → Assembled GTFs: provides
README.md - Assembled GTFs → TE fusion annotator: annotated by
README.md - Assembled GTFs → Cufflinks annotator: annotated by
README.md - Reference annotations → TE fusion annotator: guides annotation
- Intron annotations → TE fusion annotator: supplies introns
- TE fusion annotator → Transcript expression fractions: feeds expression
README.md - Cufflinks annotator → Transcript expression fractions: feeds expression
- Transcript expression fractions → Sample aggregation: processed across samples
README.md - Sample aggregation → Read command generation: defines candidates
README.md - Read command generation → samtools: queries alignments
README.md - Read command generation → Paired-read counting: dispatches counts
README.md - Single-read command generation → samtools: queries alignments
README.md - Single-read command generation → Single-read counting: dispatches counts
README.md - Paired-read counting → Candidate filtering: provides read counts
README.md - Single-read counting → Candidate filtering: provides read counts
README.md - Candidate filtering → Annotation merging: filters candidates
README.md - Reference-guided inputs → Annotation merging: provides reference set
README.md - Annotation merging → TE fusion annotator: re-annotated
README.md - Annotation merging → Cufflinks annotator: re-annotated
- TE fusion annotator → Annotation statistics: supplies annotations
README.md - Annotation statistics → Quantification summary: maps expression
README.md - StringTie → Transcript expression fractions: provides quantification
README.md - Quantification summary → Kozak translation: provides candidates
README.md - Kozak translation → Translation completion: passes sequences
README.md