-
Notifications
You must be signed in to change notification settings - Fork 5
/
cfg-autohic.txt
33 lines (26 loc) · 693 Bytes
/
cfg-autohic.txt
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
# Paths and system Settings
JOB_NAME=AutoHiC
AutoHiC_DIR=/home/ubuntu/AutoHiC
RESULT_DIR=/home/ubuntu/result
N_CPU=40
# Data options
SPECIES_NAME=At
REFERENCE_GENOME=/home/ubuntu/at/references/at.fa
# Juicer options
JUICER_DIR=/home/ubuntu/HiC/juicer
FASTQ_DIR=/home/ubuntu/at/rawdata
ENZYME=DpnII
# 3D-DNA options
TD_DNA_DIR=/home/ubuntu/3d-dna
NUMBER_OF_EDIT_ROUNDS=2
# AutoHiC options
ERROR_PRETRAINED_MODEL=/home/ubuntu/downloads/error_model.pth
CHR_PRETRAINED_MODEL=/home/ubuntu/downloads/chr_model.pth
TRANSLOCATION_ADJUST=True
INVERSION_ADJUST=True
DEBRIS_ADJUST=False
ERROR_MAX_EPOCH=5
ERROR_MIN_LEN=15000
ERROR_MAX_LEN=20000000
ERROR_FILTER_SCORE=0.9
ERROR_FILTER_IOU_SCORE=0.8