Output files#

After running LiftOn, you will obtain a LiftOn GFF3 file and a lifton_output/ directory. More details are shown in the output directory hierarchy below. This page provides guidance on how to interpret your results.

LiftOn output directory hierarchy

# LiftOn output directory hierarchy
.
├── lifton.gff3
└── lifton_output
   |
   ├── score.txt
   |
   ├── liftoff
   │   ├── liftoff.gff3
   │   ├── liftoff.gff3_db
   │   └── unmapped_features.txt
   |
   ├── miniprot
   │   ├── miniprot.gff3
   │   └── miniprot.gff3_db
   |
   ├── intermediate_files
   │   ├── proteins.fa
   │   ├── reference_all_genes.fa
   │   ├── reference_all_to_target_all.sam
   │   ├── ref_feature.txt
   │   ├── ref_transcript.txt
   │   └── transcripts.fa
   |
   └── stats
      ├── extra_copy_features.txt
      ├── mapped_feature.txt
      ├── mapped_transcript.txt
      └── unmapped_features.txt


lifton.gff3#

This is the main output of LiftOn software. It is an annotation file of the target genome in GFF3 format. Following is an example of a gene locus. For more details about GFF3, check GFF3 file format.

Example
NW_020825194.1  LiftOn  gene    15799   29728   .       +       .       ID=gene-Dmel_CG1483;Dbxref=FLYBASE:FBgn0002645,GeneID:43765;Name=Map205;cyt_map=100E3-100E3;description=Microtubule-associated protein 205;gbkey=Gene;gen_map=3-103 cM;gene=Map205;gene_biotype=protein_coding;gene_synonym=205-kDa MAP,205K MAP,205kD MAP,205kDa MAP,CG1483,Dmel\CG1483,map205,MAP205,MAP4;locus_tag=Dmel_CG1483
NW_020825194.1  LiftOn  mRNA    15799   29728   .       +       .       ID=rna-NM_001276225.1;Parent=gene-Dmel_CG1483;Dbxref=FLYBASE:FBtr0334299,GeneID:43765,GenBank:NM_001276225.1,FLYBASE:FBgn0002645;Name=NM_001276225.1;Note=Map205-RC%3B Dmel\Map205-RC%3B CG1483-RC%3B Dmel\CG1483-RC;gbkey=mRNA;gene=Map205;locus_tag=Dmel_CG1483;orig_protein_id=gnl|FlyBase|CG1483-PC|gb|AGB96532;orig_transcript_id=gnl|FlyBase|CG1483-RC;product=Microtubule-associated protein 205%2C transcript variant C;transcript_id=rna-NM_001276225.1;mutation=frameshift;protein_identity=0.795;dna_identity=0.793;status=LiftOn_chaining_algorithm
NW_020825194.1  LiftOn  exon    15799   17891   .       +       .       Parent=rna-NM_001276225.1
NW_020825194.1  LiftOn  exon    25963   26161   .       +       .       Parent=rna-NM_001276225.1
NW_020825194.1  LiftOn  exon    26586   29728   .       +       .       Parent=rna-NM_001276225.1
NW_020825194.1  LiftOn  CDS     16236   17891   2375    +       0       Parent=rna-NM_001276225.1
NW_020825194.1  LiftOn  CDS     25963   26161   221     +       0       Parent=rna-NM_001276225.1
NW_020825194.1  LiftOn  CDS     26586   28009   1649    +       2       Parent=rna-NM_001276225.1


lifton_output/#

This directory contains all LiftOn outputs, including the following:

1. score.txt#

It is a tsv file summarizing the LiftOn results.

Column definition

  1. Transcript ID

  2. Liftoff transcript protein sequence identity: \(0-1\)

  3. miniprot transcript protein sequence identity: \(0-1\)

  4. LiftOn transcript DNA sequence identity: \(0-1\)

  5. LiftOn transcript protein sequence identity: \(0-1\)

  6. The source of the annotation:

    • 'Liftoff', 'miniprot', or 'LiftOn_chaining_algorithm'.

  7. Mutation types

    • 'synonymous', 'nonsynonymous', 'inframe_insertion', 'inframe_deletion', 'frameshift', 'stop_codon_gain', 'stop_codon_loss', and 'start_codon_loss".

  8. Transcript locus coordinate: <chromosome>:<start>-<end>

Example
rna-NR_132385.2   0       0       0.9991364421416234      0       Liftoff non_coding      chr22:16314791-16352180
rna-NM_014406.5   0.9982078853046595      0.996415770609319       0.9985443959243085      0.9982078853046595      LiftOn_chaining_algorithm       frameshift      chr22:17267300-17269359
rna-NR_134584.1   0       0       0.9990338164251208      0       Liftoff non_coding      chr22:17423569-17425137
rna-NM_001318251.3        0.9910714285714286      0.9910714285714286      0.9981549815498155      0.9910714285714286      LiftOn_chaining_algorithm       frameshift      chr22:17460159-17498391
rna-NM_001386955.1        0.9910714285714286      0.9910714285714286      0.9987878787878788      0.9910714285714286      LiftOn_chaining_algorithm       nonsynonymous   chr22:17460159-17502102
rna-NM_001386956.1        0.9910714285714286      0.9910714285714286      0.997489014438167       0.9910714285714286      LiftOn_chaining_algorithm       frameshift      chr22:17460159-17502102
rna-NM_001386957.1        0.9910714285714286      0.9910714285714286      0.998533724340176       0.9910714285714286      LiftOn_chaining_algorithm       frameshift      chr22:17460159-17502102

2. liftoff/#

The liftoff GFF3 annotatation generated during the LiftOn process.


3. miniprot/#

The miniprot GFF3 file generated during the LiftOn process.


4. intermediate_files/#

In this directory, it stores all intermdeiate files, including protein sequences (FASTA), gene seuqence to genome alignment (SAM), transcript sequences (FASTA), the type of the reference gene (coding or non-coding), and the type of the reference transcript (coding or non-coding).


5. stats/mapped_feature.txt#

It is a TSV file summarizing the number of features being mapped from the reference genome to the target genome.

Column definition

  1. Feature ID

  2. The number of feature copy

  3. Feeature type: coding, non-coding, or other

Example
gene-LOC105379428 1       non-coding
gene-LOC124905168 1       other
gene-OR11H1       1       coding
gene-LOC112268291 1       non-coding
gene-POTEH        1       coding
gene-POTEH-AS1    1       non-coding
gene-PSLNR        1       non-coding

6. stats/mapped_transcript.txt#

It is a TSV file summarizing the number of transcripts being mapped from the reference genome to the target genome.

Column definition

  1. Transcript ID

  2. The number of transcript copy

  3. Transcript type: coding, non-coding, or other

Example
rna-XM_011546114.3      1       coding
rna-NM_001025161.3        2       coding
rna-XR_001755413.2        3       non-coding
rna-XR_001755415.2        3       non-coding
rna-XR_002958735.2        3       non-coding
rna-NR_110761.1   3       non-coding
id-LOC124905154   2       others

7. stats/extra_copy_features.txt#

Similar to mapped_feature.txt, this TSV file summarizes the number of additional copies of genes and indicates whether they are coding or non-coding.

Column definition

  1. Feature ID

  2. The number of feature copy

  3. Feeature type: coding, non-coding, or other

Example
gene-LOC124905154 2       other
gene-LOC107984037 3       non-coding
gene-LOC102723769 3       non-coding
gene-LOC107987323 3       non-coding
gene-LOC105372858 4       non-coding
gene-GGTLC3       3       coding
gene-LOC107985584 9       non-coding
gene-MIR650       2       other
gene-LINC02556    5       non-coding
gene-CYP2D6       2       coding
gene-LOC101927372 2       non-coding

8. stats/unmapped_features.txt#

It is a TSV file summarizing unmapped gene IDs and their types.

Column definition

  1. Gene ID

  2. Feeature type: coding, non-coding, or other

Example
gene-LOC124905174 non-coding
gene-LOC124900482 non-coding
gene-FAM246B      coding
gene-RIMBP3C      coding
gene-IGLJ1        other
gene-IGLJ2        other
gene-IGLJ3        other
gene-IGLJ4        other
gene-IGLJ5        other
gene-IGLJ6        other
gene-IGLJ7        other