-
Notifications
You must be signed in to change notification settings - Fork 0
/
PASTEClassifier.cfg
58 lines (55 loc) · 1.17 KB
/
PASTEClassifier.cfg
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
[repet_env]
pastec_version: 2.0
repet_host: mysql
repet_user: root
repet_pw:
repet_db: mysql
repet_port: 3306
repet_job_manager: SGE
[project]
project_name: <your_project_name>
project_dir: /mnt
[detect_features]
resources:
tmpDir:
term_rep: yes
polyA: yes
tand_rep: yes
orf: yes
blast: ncbiplus
TE_BLRn: no
TE_BLRtx: no
TE_nucl_bank: <bank_of_TE_nucleotide_sequences_such_as_Repbase>
TE_BLRx: no
TE_prot_bank: <bank_of_TE_amino-acid_sequences_such_as_Repbase>
HG_BLRn: no
HG_nucl_bank: <bank_of_host_genes>
TE_HMMER: yes
TE_HMM_profiles: /media/ProfilesBankForREPET_Pfam32.0.hmm
TE_HMMER_evalue: 10
rDNA_BLRn: no
rDNA_bank: <bank_of_rDNA_sequences_from_eukaryota>
tRNA_scan: no
TRFmaxPeriod: 15
clean: yes
[classif_consensus]
resources:
tmpDir:
limit_job_nb: 0
max_profiles_evalue: 1e-3
min_TE_profiles_coverage: 20
min_HG_profiles_coverage: 75
max_helitron_extremities_evalue: 1e-3
min_TE_bank_coverage: 5
min_HG_bank_coverage: 95
min_rDNA_bank_coverage: 95
min_HG_bank_identity: 90
min_rDNA_bank_identity: 90
min_SSR_coverage: 75
max_SSR_size: 100
remove_redundancy: no
min_redundancy_identity: 95
min_redundancy_coverage: 98
rev_complement: no
add_noCat_bestHitClassif: no
clean: yes