Usage

Input files

GTF files:
    GTF files which could be generated by stringtie from short-read RNA-seq.
BW files:
    Two compressed BW files, containing CPM-normalized coverage for uniquely mapped and multi-mapped RNA-seq reads, which could be generated by deepTools.
TE reference bed:
    TE annotation in BED format (at least 6 fields: chrom, chromStart, chromEnd, ID, name, and strand).
Reference GTF:
    Reference GTF file for gene annotations.
Reference fasta file:
    A FASTA file containing chromosome or scaffold nucleotide sequences.
Chromosome length file:
    A text file containing chromosome lengths.

TEIRI_correct.py

TEIRI_correct.py predicts transcript TSSs using the deep-learning model.

usage: TEIRI_correct.py [-h] [--input INPUT] [--short_path SHORT_PATH] [--chr_len CHR_LEN] [--window_length WINDOW_LENGTH] [-g REF_FA] [-m MODEL_PATH] [-p PREFIX]

TEIRI_correct

options:
  -h, --help            show this help message and exit
  --input INPUT         Prefix of input files (required)
  --short_path SHORT_PATH
                        Path to input files (default: '.')
  --chr_len CHR_LEN     Chromosome length file (required)
  --window_length WINDOW_LENGTH
                        Window size for TSS prediction (default:10000)
  -g REF_FA, --ref_fa REF_FA
                        Reference fasta file (required)
  -m MODEL_PATH, --model_path MODEL_PATH
                        Path to the deep-learning model (required)
  -p PREFIX, --prefix PREFIX
                        Prefix for output files (default: TEIRI)

TEIRI_merge.py

TEIRI_merge.py identifies TE-initiated transcripts and merges transcripts across samples with a reference-guided strategy.

usage: TEIRI_merge.py [-h] [-i GTF_LIST] [-r REFERENCE_GTF] [--TE_anno TE_ANNO] [--tss_window TSS_WINDOW] [--max_tss MAX_TSS]
                      [--min_NGS_samples MIN_NGS_SAMPLES] [--max_transcripts MAX_TRANSCRIPTS]
                      [--trunctated_exclude TRUNCTATED_EXCLUDE] [--min_transcript_length MIN_TRANSCRIPT_LENGTH]
                      [--threshold THRESHOLD] [-p PREFIX]

TEIRI_merge

TEIRI_consolidate.py

TEIRI_consolidate.py consolidates and annotates TE-initiated transcripts.

usage: TEIRI_consolidate.py [-h] [-i GTF_LIST] [-r REFERENCE_GTF] [--TE_anno TE_ANNO]
                            [--tss_merge_distance TSS_MERGE_DISTANCE] [--min_exon_length MIN_EXON_LENGTH] [-p PREFIX]

TEIRI_consolidate