1.2. Output Contents (FastDTLmapper)

Output Contents

In this page, explain output contents of following 5 files in 03_aggregate_map_result.

.
├── 00_user_data/  
├── 01_orthofinder/ 
├── 02_dtl_reconciliation/  
├── 03_aggregate_map_result/  -- Genome-wide DTL reconciliation aggregated and mapped results
│   ├── all_dtl_map.nwk              -- Genome-wide DTL event mapped tree file
│   ├── all_gain_loss_map.nwk        -- Genome-wide Gain-Loss event mapped tree file
│   ├── all_og_node_event.tsv        -- All OG DTL event record file
│   ├── all_transfer_gene_count.tsv  -- All transfer gene count file
│   └── all_transfer_gene_list.tsv   -- All transfer gene list file
└── log/

1. all_dtl_map.nwk

Genome-wide DTL event mapped tree file.
Each node DTL map data is described in following format.

NodeID | GeneNum [brn=BornNum dup=DuplicationNum los=LossNum trn=TransferNum]

Example of all_dtl_map.nwk:

((outsp1 | 507 [brn=13 dup=21 los=28 trn=0]:0.107239,outsp2 | 691 [brn=76 dup=107 los=0 trn=7]:0.107239)N002 | 501 [brn=82 dup=3 los=0 trn=2]:0.306859,((insp1 | 664 [brn=32 dup=25 los=19 trn=7]:0.027931,insp2 | 747 [brn=57 dup=82 los=13 trn=2]:0.027931)N004 | 619 [brn=119 dup=10 los=46 trn=0]:0.324618,(insp3 | 1026 [brn=274 dup=151 los=28 trn=2]:0.243408,(insp4 | 673 [brn=61 dup=54 los=35 trn=0]:0.113100,insp5 | 660 [brn=40 dup=42 los=20 trn=5]:0.113100)N006 | 593 [brn=33 dup=2 los=71 trn=2]:0.130308)N005 | 627 [brn=98 dup=7 los=14 trn=0]:0.109141)N003 | 536 [brn=121 dup=1 los=0 trn=0]:0.061550)N001 | 414 [brn=414 dup=0 los=0 trn=0];

Use SeaView to visualize it as shown below.

2. all_gain_loss_map.nwk

Genome-wide Gain-Loss event mapped tree file.
Each node gain/loss map data is described in following format.

NodeID | GeneNum [gain=GainNum los=LossNum]

Example of all_gain_loss_map.nwk:

((outsp1 | 507 [gain=34 los=28]:0.107239,outsp2 | 691 [gain=190 los=0]:0.107239)N002 | 501 [gain=87 los=0]:0.306859,((insp1 | 664 [gain=64 los=19]:0.027931,insp2 | 747 [gain=141 los=13]:0.027931)N004 | 619 [gain=129 los=46]:0.324618,(insp3 | 1026 [gain=427 los=28]:0.243408,(insp4 | 673 [gain=115 los=35]:0.113100,insp5 | 660 [gain=87 los=20]:0.113100)N006 | 593 [gain=37 los=71]:0.130308)N005 | 627 [gain=105 los=14]:0.109141)N003 | 536 [gain=122 los=0]:0.061550)N001 | 414 [gain=414 los=0];

Use SeaView to visualize it as shown below.

3. all_og_node_event.tsv

All OG(Ortholog Group) DTL event record tsv format file (See example data here).

Columns	Contents
OG_ID	OG(Ortholog Group) ID generated by OrthoFinder
NODE_ID	Species tree node id
GENE_NUM	OG-Node gene number
GAIN_NUM	OG-Node gain number (Gain=Brn+Dup+Trn)
BRN_NUM	OG-Node born number
DUP_NUM	OG-Node duplication number
TRN_NUM	OG-Node transfer number
LOS_NUM	OG-Node loss number
TRN_DETAIL	Transer path list (e.g. 'N023 -> N012,N011 -> N008')

4. all_transfer_gene_count.tsv

All transfer gene count tsv format file (See example data here).
Gene transfer information is extracted from AnGST result file.

Columns	Contents
TRANSFER_PATH	Transfer path (e.g. 'N023 -> N012')
TRANSFER_DERIVED_GENE_NUM	Transfer derived gene number in TRANSFER_PATH
TRANSFER_DERIVED_GENE_ID_LIST	Transfer derived gene id list in TRANSFER_PATH

5. all_transfer_gene_list.tsv

All transfer gene list tsv format file (See example data here).
Gene transfer information is extracted from AnGST result file.

Columns	Contents
OG_ID	OG(Ortholog Group) ID
TRANSFER_DERIVED_GENE_ID	Transfer derived gene id
TRANSFER_PATH	Transfer path (e.g. 'N023 -> N012')